http://www.bx.psu.edu/~ratan/

Address of the bookmark: http://www.bx.psu.edu/miller_lab/

1. Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
2. Reducing/removing reference bias as compared to mapping based approaches.

The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.

https://ibest.github.io/ARC/

Address of the bookmark: https://ibest.github.io/ARC/

Gene expression and protein expression patterns between normal and non-normal tissues is a growing area of research that may lead to the identification of candidate genes for understanding the etiology of common, complex diseases.

Lab homepage @ http://ritchielab.psu.edu/ritchielab/

Address of the bookmark: http://www.gigasciencejournal.com/content/2/1/15?utm_content=buffer25ee0&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

1. Strand NGS
   • offers many different tools including alignment, RNA-Seq, DNA-Seq, ChIP-Seq, Small RNA-Seq, Genome Browser, visualizations, Biological Interpretation, etc. Supports workflows “one can import the sample data in FASTA, FASTQ or tag-count format. In addition, prealigned data in SAM, BAM or Illumina-specific ELAND format can be directly imported for analysis.”
   • Alignment feature: Supports alignment from Illumina, Ion Torrent, 454 (Roche), and Pac Bio
   • DNA-Seq Feature, can annotate with dbSNP
2. CLC Genomics Workbench
   
   • (QIAGEN). Features include: resequencing, workflow, read mapping, de novo assembly, variant detection, RNA-Seq, ChIP-Seq, Genome Browser, etc (entire list on website); Main Workbench offers database search (Genbank, Blast, Pubmed); 2000 organizations have invested in CLC
   • Accepts VCF files from 1000 Genomes Project
   • Accepts downloaded tracks from dbSNP
   • Also accepts: FASTA, GFF/GTF/GVF, BED, Wiggle, Cosmic, UCSC variant database, complete genomics master var file
   • Read mapping: “In addition to Sanger sequence data, reads from these high-throughput sequencing machines are supported: The 454 FLX System and the 454 GS Junior System from Roche, Illumina Genome Analyzer, Illumina HiSeq, Illumina HiScan, and Illumina MiSeq sequencing systems, SOLiD system from Life Technologies, Ion Torrent system from Life Technologies, Helicos from Helicos BioSciences”
   • De novo assembly: “In addition to Sanger sequence data, reads from these high-throughput sequencing machines are supported The 454 FLX System and the 454 GS Junior System from Roche, Illumina Genome Analyzer, Illumina HiSeq, Illumina HiScan, and Illumina MiSeq sequencing systems, SOLiD system from Life Technologies, Ion Torrent system from Life Technologies”
   • Annotation tracks from Ensembl
3. DNAnexus
   • Private cloud repository -- formerly a redistributor of SRA and other NCBI resources; command-line or via web, can fetch data from a URL, build custom pipeline/ workflow has sra.dnanexus.com site: data downloads come directly from NCBI
4. Ingenuity Variant Analysis
   • (QIAGEN) allows for variant identification and analysis, uses NCI-60 data set for cancer, Supported third part informatin: Entrez Gene, RefSeq, ClinVar; gives contextual details of results instead of just A to B relationship
   • Has own database-- “knowledge base” based on COSMIC, OMIM, and TCGA databases
5. Lasergene Genomics Suite
   • Comprehensive NGS software pipeline for assembly, alignment, variant calling and analysis of NGS data
   • Supported workflows include: reference-guided and de novo genome and transcriptome assembly and analysis, metagenomics sample assembly, targeted resequencing, exome alignment, gene panels with validation control, variant analysis, and RNA-Seq, ChIP-Seq and miRNA alignment and analysis.
   • #1 in accuracy: fewer false negatives and better sensitivity compared to results obtained from other aligners
   • Aligns exome data and performs variant calling an average of 3 times faster than alternative pipelines
   • Annotates genomic data with allele and genotype frequency, functional impact predictions, evolutionary conservation scores and pathogenicity
   • Supports all major NGS technologies (Illumina, Ion Torrent, Pac Bio and Roche 454) and project types
   • Available on Windows, Mac OS X, Linux, and the Amazon Cloud
6. NextGENe
   • “perfect analytical partner for the analysis of desktop sequencing data produced by the ION PGM™, Roche Junior, Illumina MiSeq as well as high throughput systems as the Ion Torrent Proton, Roche FLX, Applied BioSystems SOLiD™ and Illumina® platforms.” runs on Windows, free-standing multi-application package-- SNP/Indel analysis, CNV prediction and disease discovery, whole genome alignment, etc.
   • Data can be imported from Clinvar, dbSNP, Genbank:http://www.softgenetics.com/PDF/NextGene_UsersManual_web.pdf
7. Partek Genomics Suite
   • Cited in over 3,500 peer-reviewed scientific publications
   • Workflows for microarray and PCR data include: Gene expression including alternative splicing, miRNA expression, Genome Wide Association Studies, Mother-Father-Child Trio analysis, DNA Copy number including allele specific copy number and Loss of Heterozygosity (LOH), and ChIP, and methylation. Next Generation Sequencing (NGS) workflows include: RNA-Seq, miRNA-Seq, ChIP-Seq, DNA-Seq, and Methylation
   • Powerful statistics and interactive, publication ready visualizations
   • Supports all commercial next generation sequencing and microarray file format as well as text files
   • Can input GEO SOFT files
8. Partek Flow
   • Installation can be cloud-based or on a local cluster or Linux server
   • Easy to use point-and-click interface
   • Takes NGS data (.fastq, BAM, SAM), microarrays (Affymetrix, Illumina) and text files
   • Supports custom genome builds and annotation databases
   • Performs base trimming, alignment, quantification, quality analysis, statistics, and visualization
   • Includes ten fully customizable aligners (Bowtie, Bowtie 2, BWA, GSNAP, Isaac 2, SHRiMP 2, STAR, TMAP, TopHat and TopHat 2)
   • Applications for RNA-Seq, Small RNA-Seq, WGS/WES, Pathway enrichment, Fusion detection and Variant calling
   • Allows users to create, save, share, or download analysis pipelines for automated and repeatable analysis
   • Collaborate with others without transferring data
   • Integrates microarray and next generation sequencing data
9. Golden Helix: SNP and Variation Suite
   • used for managing, analyzing and visualizing genotypic and phenotypic data; Features: Genome-wide association studies, genomic prediction, copy number analysis, small sample DNA-Seq workflows, large sample DNA-seq analysis, RNA-seq analysis. Supported files: .txt, excel XLS & XLSX, CEL, CHP, CNT, Illumina, Plink PED, TPED, BED, Agilent files, NimbleGen data summary files, VCF files, Impute2 GWAS files, HapMap format, MACH output, + 50 other formats consumes NCBI data directly
10. Genomatix
    • Applications: ChIP-Seq, DNA-Seq, RNA-Seq, DNA methylation; enable personalized medicine,
    • Mining Stations: Supports all established NGS sequencing platforms- SOLiD, 454 Life Sciences, Genome Analyzer, HiSeq, MiSeq, IonTorrent
    • Software Suite: can upload sequence of BED files
    • Genome browser: BED and BAM files, Public data- 1500 BED files available for every user
11. Biodatomics
    • Open source platform (SaaS), analysis and genome sequencing tools, integrates over 400 genomic analysis open source tools and pipelines, have a private and public cloud version. Features: genomic data visualization, drag and drop interface, accelerated analysis, real-time collaboration
    • They have a couple modules to do so, and have enabled parts of the sra toolkit
12. SolveBio
    • Software product, for clinical genomics professionals, manage, curate, report genomic variation
    • Has own data library -- data from NCBI
13. Basepair
    • Offers high quality workflows for all common NGS applications (RNA-Seq, ChIP-Seq, DNA-Seq, etc.)
    • Very fast - get all results in a 1-2 hours. Cloud-based, no storage or computing limits.
    • Easy to use - less than a minute to run an analysis
    • REST and Python API to mange large projects.
     

Variant Identification

Germline Callers

1. IMPUTE2
   • Description: phasing observed genotypes and imputing missing genotypes uses reference panels to provide all available halotypes, does not use population labels or genome-wide measures; designed to represent variation in one population; Fairly popular
   • Input:
   • Reference Haplotypes: Links to 1000 Genomes and HapMap downloads
   • Output:
2. FreeBayes
   • Description: finds SNPs, Indels, MNPs; reports variants based on alignment; haplotype based
   • Input: BAM- uses BAMtools API to parse
   • Reference genome: FASTA
   • Output: VCF
3. SOAPindel
   • Description: detects indels from NGS paired-end sequencing
   • Input: files with read alignment can be SOAP or SAM formats, users must also give raw reads in Fasta or Fastq
   • Reference Sequence used to align reads: FASTA
   • Output:
4. 2Kplus2
   • Description: algorithm searches graphs produced by de novo assembler Cortex; c++ source code for SNP detection “2kplus2.cpp is a c++ source code for the detection and the classification of single nucleotide polymorphisms in transformed De Bruijn graphs using Cortex assembler.”
   • Input:
   • Output:
5. Atlas 2
   • Description: specializes in separation of true SNPs and indels from sequencing and mapping errors, last update January 2013
   • Input: takes BAM file,
   • Reference Genome: FASTA
   • Output: produces VCF
6. CRISP
   • Description: identifies SNPs and INDELs from pooled high-throughput NGS, not used for analysis of single samples; implemented in C and uses SAMtools API; latest version should work with diploid genomes
   • Input: requires BAM files (aligned with GATK)
   • Reference Genome: indexed FASTA file
   • Output: VCF files
7. Dindel
   • Description: (Wellcome Trust Sanger) calls small indels from short-read sequences, only can handle Illumina data; cannot test candidate indels; written in C++, used on Linux based and Mac computers (not tested in windows)
   • Input: BAM files
   • Output: VCF
8. discoSnp++
   • Description: detects homozygous and heterozygous SNPs and Indels; software composed of 2 modules (kissnp2 and kissreads)
   • Input: raw NGS datasets; fasta, fastq, gzipped or not;
   • no reference genome required; read pairs can be given
   • Output: FASTA
9. FamSeq
   • Description: family-based sequencing studies- provides probability of an individual carrying variant based on family’s raw measurements; accommodates de novo mutations, can perform variant calling at chrX;
   • Input: VCF
   • Output: VCF
10. GeneticThesaurus
    • Description: “Annotation of genetic variants in repetitive regions”
    • Input: Initial variant calling from bam → vcf output
    • Reference Genome: need to provide own fasta file for hg19 genome,
    • Output: vcf.gz, vtf.gz, and baf.tsv.gz output
11. glfMultiples
    • Description: command-line, variant caller
    • Input: GLF
    • Output: VCF
12. glfSingle
    • Description: uses likelihood-based model for variant calling, starts from genotype likelihoods that have been computed from other tools (ex. Samtools BAQ), the likelihoods combine with individual-based prior p(genotype) to generate posterior probabilities
    • Input: GLF
    • Output: VCF
13. Halvade
    • Description: command-line; written in Java, “to run halvade a reference is needed for both GATK and BWA and a SNP (dbSNP!) database is required
    • Input: FASTQ
    • Output: VCF
14. indelMINER
    • Description: identifies indels from paired-end reads
    • Input: BAM (aligned in SAMtools API)
    • Output: VCF
15. Indelocator
    • Description: (Broad Institute): does not perform realignment, relies on alignments in BAM files (BAM files need aligned before put into indelocator); recommended to use GATK prior;
    • Input: 2 BAM files(tumor & normal), annotated as germline or somatic; also has single sample mode
    • Output: “Output of Indelocator is a high-sensitivity list of putative indel events containing large numbers of false positives. The statistics reported for each event have to be used to custom-filter the list in order to lower false positive rate”
16. Isaac Variant Caller
    • Description: detects SNPs and small indels from diploid sample; designed to run on “nux-like platforms”
    • Input: BAM
    • Output: VCF
17. KvarQ
    • Description: in silico genotyping for selected loci in bacterial genome, written in Python and C
    • Input: FASTQ
    • reference genome or de novo assembly not needed
    • Output:
18. LoFreq
    • Description: SNV caller, Python language, standalone program, uncovers cell-population heterogeneity from high-throughput sequencing datasets; calls variants found in <.05% of the population
    • Input: BAM file input→ suggest running through GATK
    • Output:
19. Manta
    • Description: Calls indels and SVs from paired end reads; standalone, command line program; Written in C++ and Python
    • Input: BAM (can tolerate non-paired-end reads); a matched tumor sample may be provided as well
    • Output: VCF
20. MarginAlign
    • Description: SNV caller, specifically tailored to Oxford Nanopore Reads, written in Python; Package comes with 3 programs, marginAlign, marginCaller (calls SNVs), marginStats (computes qc stats on sam files)
    • Input: SAM
    • Output: SAM
21. MendelScan
    • Description: Last release March 2014; for analyzing sequencing data in family studies of inherited diseases; variant calls for a family in VCF file; still in alpha-testing on github, example data uses 1000 genomes dataset
    • Input:
    • Output:
22. nanopore
    • Description: UCSC Nanopore group (group at UCSC studying using ion channels for analysis of single RNA/DNA structures) software pipeline; tailored to Oxford Nanopore Reads; command line program
    • Input: FASTQ
    • Reference files: FASTA
    • Output: “For each possible pair of read file, reference genome and mapping algorithm an experiment directory will be created in the nanopore/output directory.”
23. Platypus
    • Description: Package program, written in C, Python, Cython; Can identify SNPs, MNPs, short indels, and larger variants; has been tested on very large datasets (1000 genomes)
    • Input: BAM
    • Reference Genome: FASTA (files must be indexed using Samtools or similar program
    • Output: VCF
24. QualitySNPng
    • Description: detection of SNPs; “can be used as a standalone application with graphical user interface as part of pipeline system”; does not require fully sequenced reference genome; haplotype strategy
    • Input:SAM, ACE
    • Output: GUI
25. ReviSTER
    • Description: command line program; automated pipeline; utilizes BWA, BLAT, and SAMTools; utilizes BWA mapping program;
    • Input: FASTQ,
    • Reference sequence file and list file containing STR locations as inputs
    • Output: SAM
26. RVD
    • Description: command-line program, detection of rare SNVs, relies upon Samtools, can be run in MATLAB
    • Input: BAM
    • Reference Genome: FASTA
    • Output: “The algorithm output is a call table -- a comma-separated file with one line for each base position and each line in the following format:
    • AlginmentReferencePosition, AlignmentBase, Call ,SecondBase, CenteredErrorPrc, ReferenceErrorPrc, SecondBasePrc”
27. SNVer
    • Description: calls common and rare variants in pool or individual NGS data, reports overall p-value, operating system independent statistical tool, identifies SNPs and INDELs, written in Java, no dependencies, straightforward command-line
    • (SNVerGUI=GUI version) --SNVerGUI: desktop tool for variant detection
    • Input: chrX annotation, sam.zip, bam.zip
    • reference file must be aligned to the data file
    • Output:
28. SNVMix
    • Description: detects SNVs from NGS, post-alignment tool
    • Input: pileupformat (Maq or Samtools)
    • Output:
29. SV-M
    • Description: Structural Variant Machine - predicts indels, uses split read alignment profiles, validated by Sanger Sequencng
    • Input:paired-end Illumina reads from 1001 genomes project (uses ref plant- 1001genomes.org)
    • Ouptut:
30. SNPest
    • Description: Standalone program, language C++, Perl
    • Input: mpileup (SAMtools)
    • Output: VCF
31. TrioCaller
    • Description:Command line program, relies on BWA and samtools; genotype calling for unrelated individuals and parent-offspring trios
    • Input: BAM (that has been aligned in BWA and Samtools
    • Output: BCF that can be formatted to VCF using bcftools
32. Snippy
    • Description: finds indels between haploid reference genome and NGS sequence reads
    • Input:read files- FASTQ or FASTA (can be .gz compressed), output- .aln, .tab, .txt
    • Reference genome in FASTA or GENBANK
    • Output:
33. VntrSeek
    • Description: pipeline for discovering microsatellite tandem repeats with high-throughput sequencing data
    • Input: gzip-compressed FASTA or FASTQ
    • Output: VCF files; one for TRs and observed alleles, another file contains link to viewer

Somatic Callers

1. Cake
   • Description: standalone program, “pipeline for the integrated analysis of somatic variants in cancer genomes”; integrates four algorithms; written in Perl; required tools: samtools, tabix, vcftools, VarScan2, bambino, cmake, somaticsniper (User guide; workflow page)
   • Input: tumor and normal reads in BAM files, run through variant calling programs to generate intermediate VCF
   • Output: VCF
2. MuTect
   • Description: Broad Institute, identification of somatic point mutations in cancer genomes; requires preprocessing of reads (GATK)
   • Input: same as GATK (FASTA reference genome, SAM read files)
   • Output: call-stats, VCF, wiggle files
3. Polymutt
   • Description: calls SNVs and detects de novo point mutations in families
   • Input: GLF or BAM or VCF (must have identical chromosome orders)
   • Output: VCF
4. Bassovac
   • Description: Improved Bayesian inversion somatic caller; unlike other software packages, treats effects fully probabilisticallys instead of using ad-hoc modeling; effects are integrated at the atomic level and standard probability theory integrates read tallies to the sample level and to the tumor-normal pair level; "pending public release"
   • Input:
   • Output:
5. CLImAT
   • Description: standalone program; “accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole genome sequencing data”
   • Input: depth file generated by DFExtract and a config file
   • Output: .results file, .Gtype, LOG.txt, also generates visualization
6. DeNovoGear
   • Description: de-novo variant calling and interpretation; standalone program; dependencies C++ compiler, CMake, HTSlib, Eigen, Boost
   • Input: PED and BCF
   • Output: “The output format is a single row for each putative de novo mutation (DNM), with the following fields”
7. EBCall
   • Description: Empirical Baysian Mutation Calling; standalone program; uses tumor/normal paired reads and non-paired normal reference samples; dependent on samtools, R and VGAM pack for R
   • Input: BAM
   • Output: not sure what exact type of file- “The format of the result is suitable for adding annotation by annovar.”
8. HapMuc
   • Description: standalone program; “utilizes the information of heterozygous germline variants near candidate mutations”; Dependent upon- Boost, SAMtools, BEDtools; 3 step workflow
   • Input: BAM
   • Output: BED
9. MultiGeMS
   • Description: Multi-sample Genotype Model Selection
   • Input: .txt, pileup (SAM/BAM converted to pileup format)
   • Output: VCF
10. MultiSNV
    • Description: command-line program; calls SNVs from NGS data from multiple samples from the same patient; dependent on R, Git, cmake, Boost and compile libraries
    • Input: BAM or pileup
    • Output: VCF
11. MutationSeq
    • Description: standalone program, somatic SNV detection in tumor/normal samples; dependent on python, bamtools, boost, and LAPACK
    • Input: BAM
    • Output: VCF4.1 consisting of two parts (meta information & data lines)
12. qSNP
    • Description: standalone program; SNV caller for somatic variants in “low cellularity cancer samples”
    • Input: BAM, dbSNP data, Illumina data, chrConv
    • Output: “qSNP output files are named using a 4-element pattern: ...”
13. RADIA
    • Description: RNA and DNA Integrated Analysis for Somatic Mutation Detection; DNA only Method(tumor/normal pair, ignores RNA) or Triple BAM Method (uses all three datasets from same patient); dependent upon python, samtoools, pysam API, BLAT, SnpEff
    • Input: BAM
    • Reference Genome: FASTA indexed with SAMtools faidx
    • Output: VCF
14. RVD2
    • Description: sensitive, variant detection for low-depth targeted NGS data; python module or command- line program;
    • Input: tab- deliminted depth chart format (converted from pileup files)
    • Output: three hdf5 files and a vcf file
15. Shimmer
    • Description: standalone program; detects somatic SNVs with multiple testing correction, uses Fisher’s exact test; dependent on git, samtools, R, R statmod package; for tumor/normal matched samples
    • Input: BAM
    • Output: VCF
16. SNV-PPILP
    • Description: Refines GATK’s Unified Genotyper SNV calls for “multiple samples assumed to form a phylogeny”
    • Input:
    • Output:
17. SomaticSniper
    • Description: command-line application to identify SNPs between tumor/normal pairs- predicts probability of difference between two
    • Input: BAM
    • Reference Genome in FASTA
    • Output: VCF
18. Strelka
    • Description: somatic variant calling workflow for matched tumor-normal samples; detects indels; runs on *nux-like platform
    • Input: BAM (must be sorted and indexed)- Strelka does own realignment around indels-- don’t need to do this type of pre-processing
    • Output: pair of VCF files
19. Triodenovo
    • Description: Bayesian framework for calling de novo mutations in trios
    • Input: VCF file with PL or GL fields (recommend using GATK or samtools to generate)
    • Output: out_vcf
20. UNCeqr
    • Description: finds somatic mutations using integration of DNA and RNA seq data-- boosts sensitivity for low purity tumors and rare mutations;
    • Input:”can accept a variety of sequencing inputs and configurations”
    • Output: “table of somatically mutated sites and associated information. These somatic mutations can be annotated with predicted transcript and protein effects using third party tools, such as Annovar”
21. Virmid
    • Description: Virtual Microdissection for SNP calling; Java based; for disease-control matched samples; uncovers SNPs with low allele frequency by considering alpha contamination
    • Input: BAM (must be sorted and indexed- samtools sort)
    • Output: VCF and report file

Germline + Somatic Callers

1. VarScan 2
   • Description: identify germline variants, private and shared variants, somatic mutations, and somatic CNVs; detects indels
   • Input: SAMtools pileup
   • Output: VCF
2. BAYSIC
   • Description: Bayesian method; combines variant calls from different methods (GATK, FreeBayes, Atlas, Samtools, etc)
   • Input: VCF format from one or more variant calling programs
   • Output: VCF file containing integrated set of variant calls
3. MSIsensor
   • Description: Microsatellite instability detection; C++ program, detects somatic and germline variants in tumor-normal paired data
   • Input: BAM index files (normal and tumor)
   • Output:
4. Beagle version 4
   • Description: software package: genotype calling, phasing, imputation of ungenotyped markers, and identity-by-descent segment detection:unsure if this one is in the right category; genotype calling, phasing, imputation of ungenotyped markers, and identity-by-descent segment detection;
   • Input: VCF
   • Output: VCF
5. QuadGT
   • Description: software package, SNV calling from normal-tumor pair and two parent genomes; quantifies descent-by-modification relationships; Written in Java
   • Input: BAM files (parsed by Picard/Samtools API)
   • Reference Genome; FASTA
   • Output: VCF
6. RAREVATOR
   • Description: RAre REference VAriant annotaTOR; command line; “identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data”; Bayesian genotype likelihood model
   • Input: BED or VCF files from GATK
   • Output: two VCF files (one for SNVs, one for Indels)
7. Scalpel
   • Description: Used for detecting indels in a reference genome; performs localized micro-assembly of specific regions of interest; can do single, de novo, somatic reads; requires that raw reads are aligned with BWA
   • Input: BAM
   • Output: either VCF or ANNOVAR
8. SOAPsnp
   • Description: based on Baye’s theorem; calls consensus genotype
   • Input:SOAP short read alignment results
   • Output: GLF, option of flat tabular format
9. VariantMaster
   • Description: “extract causative variants for monogenic and sporadic genetic diseases”; uses ANNOVAR;
   • Input: BAM or VCF files (from SAMtools, GATK)
   • Output:

Downstream Analysis of Variants

1. PrediXcan
   • Description: command-line, standalone package program; available in Perl, Python, and R versions; predicts liklihood of a gene being related to a certain phenotype- “that directly tests the molecular mechanisms through which genetic variation affects phenotype.”; no actual expression data used, only in silico expression; “PrediXcan can detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations.”
   • Input: genotype and phenotype file (doesn’t specify file type)
   • Output:default values: genelist, dosages (file format: snpid rsid) , dosage_prefix, weights, output
2. ATHENA
   • Description: Analysis Tool for Heritable and Environmental Network Associations; software package, combines machine learning model with biology and statistics to predict non-linear interactions
   • Input: Configuration file, Data file, Map file (includes rsID)
   • Output: Summary file, Best model file, dot file, individual score file, cross-validation file
3. CCRaVAT and QuTie
   • Description: (Wellcome Trust Sanger) Case-Control Rare Variant Analysis Tool and Quantitative Trait; software packages for large-scale analysis of rare variants
   • Input: PED file and MAP file
   • Output: Five tab-delimited txt files
4. GCTA
   • Description: Genome Wide Complex Trait Analysis; package program, command line interface; estimates variance by all SNPs; 5 main functions: “data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation”
   • Input: PLINK binary PED files, MACH output format
   • Output:
5. GenomeComb
   • Description: package for analysis of complete genome data; annotation using public data or custom tracks, automated primer desing for Sanger or Sequenom validation; “The cg process_illumina command can be used to generate annotated multisample data starting from fastq files, using tools such as bwa for alignment and GATK and samtools for variant calling. Sequencing data can also be imported from Complete Genomics (cg_process_sample command), Real Time Genomics (cg_process_rtgsample command) and VariantCallFormat (VCF) variant files (vcf2sft command).”
   • Input: Sequencing data from Complete Genomics, Illumina, SOLiD and VCF;
   • Output: standard file format used is a simple tab delimited file (.sft, .tsv)
6. Genome Track Analyzer
   • Description: compares genome tracks; allows user to compare DNA expression/binding;
   • Input: multiple: SGR/TXT, BED, BED6, GFF; if using prealigned sequence data- use MACS peak caller: BAM, BED, SAM, ELAND
   • Output:
7. GVCBLUP
   • Description: animal gene mapping; “genomic prediction and variance component estimation of additive and dominance effects”; standalone program, command line interface, writting in C++ and Java
   • Input:
   • Output:
8. HOMOG
   • Description: Analyzes heterogeneity with respect to single marker loci or known maps of markers; Carries out homogeneity test for alternative hypothesis “Two family types, one with linkage betweeen a trait to a marker or map of markers, the other without linkage”
   • Input: HOMOG.DAT - described on website
   • Output: HOMOG.OUT
9. INTERSNP
   • Description: GWIA for case-control SNP and quantitative traits; selected for joint analysis using priori information; Provides linear regression framework, Pathway Association Analysis, Genome-wide Haplotype Analysis,
   • Input: PLINK input formats (ped/map, tped/tfam, bed/bim/fam) Compatible with SetID files
   • Gene reference file: Ensembl Release 75
   • Output: covariance matrix for regression models
10. mtSet
    • Description: Currently only the standalone version available, but moving to LIMIX software suite; offers set tests- allows for testing between variants and traits; accounts for confounding factors ex. relatedness
    • Input: sample-to-sample genetic covariance matrix needs to be computed; multiple types of input; simulator requires input genotype and relatedness component;
    • Output: resdir (result file of analysis), outfile (test statistics and p-values), manhattan_plot (flag)
11. MultiBLUP
    • Description: Package program, command line interface; constructs linear prediction models; Best Linear Unbiased Prediction; improves upon BLUP involving kinship matrices; options: pre-specified kinships, regional kinships, adaptive multiblups, LD weightings
    • Input: PLINK format
    • Output:.reml, .indi.blp

Variant Annotation

1. ANNOVAR
   • Description: command-line tool, supports SNPs, INDELs, CNVs and block substitutions, provides wide variety of annotation techniques, depends upon multiple databases (each needing to be downloaded); annotates genetic variants; utilizes RefSeq, UCSC Genes, and the Ensembl gene annotation systems; can compare mutations detected in dpSNP or 1000 Genomes Project; Very popular *“The final command run TABLE_ANNOVAR, using dbSNP version 138, 1000 Genomes Project 2014 Oct version, NIH-NHLBI 6500 exome database version 2 (referred to as esp6400siv2), dbNFSP version 2.6 (referred to as ljb26), dbSNP version 138 (referred to as snp138) databases and remove all temporary files, and generates the output file called myanno.hg19_multianno.txt”
   • Input: VCF, ANNOVAR input format (simple text-based format); can convert other formats into ANNOVAR input format
   • Output: VCF (if input VCF), output file with multiple columns, tab-delimited output file
2. wANNOVAR
   • provides web-based access to ANNOVAR software
3. PolyPhen-2
   • Description: Very popular; Polymorphism Phenotyping; Web application; predicts impact of amino acid substitution on protein; Calculates Bayes posterior probability (Last update July 2015)
   • Input: FASTA
   • Output:
4. SIFT
   • Description: predicts how an amino acid substitution will affect protein function; Based on degree of conservation of amino acid residues- collected though PSI-BLAST; can be applied to nonsynonymous polymorphisms or laboratory-induced missense mutations; links to dbSNP 132, GRCh37; Standalone or web app program; Very popular
   • Input: Uniprot ID or Accession, Go term ID, Function name, Species Name or ID, etc
   • Output:
5. snpEff
   • Description: Genetic variant annotation and effect prediction toolbox; integrated with Galaxy, GATK, and GNKO; can annotate SNPs, INDELs, and multiple-nucleotide polymorphisms; categorizes effects into classes by functionality; Very popular; Standalone or Web app; Claims to calculate all SNPs in 1000 genomes (EMBI) in less than 15 minutes; can annotate SNPs, MNPs, and insertions and deletions; Provides assessment of impact of the variant ( low, medium or high)
   • Input: VCF, BED
   • Output: VCF (with new ANN field, also used in ANNOVAR and VEP), HTML summary files
6. SnpSIFT
   • Description: Filter and manipulate annotated files; Part of SnpEff main distribution; one variants have been annotated, this can be used to filter your data to find relevant variants
   • Input:
   • Output:
7. VAAST 2
   • Description: Variant Annotation, Analysis, and Search Tool; probabilistic search tool for identifying damage genes and the disease causing variants; can score both coding and non-coding variants; Four tools: VAT (Variant annotation tool), VST (Variant Selection Tool), VAAST, pVAAST (for pedigree data); updated April 2015
   • Input: FASTA, GFF3, GVF
   • Output: CDR (condenser file), VAAST file (both unique to VAAST)
8. VEP
   • Description: (Ensembl) Variant Effect Predictor; determines effect of variants on genes, transcripts, and protein sequence; uses SIFT and PolyPhen
   • Input: Coordinates of variants and nucleotide changes; whitespace- separated format, VCF, pileup, HGVS
   • Output: VCF, JSON, Statistics
9. ABSOLUTE
   • Description: (Broad Institute); can estimate purity and ploidy to compute absolute copy number and mutation multiplicitie; reextracts data from the mixed DNA population
   • Input: HAPSEQ segdat or segmentation file
   • Output: per-sample output directory and subdirectory providing per-sample text files containing standard out being emitted from R
10. Alamut Batch
    • Description: high-throughput annotation software for NGS analysis; for “intensive variant analysis workflows”; “enriches raw NGS variants with dozens of attributes”; based on clinically oriented Alamut database; Supports human genes; easy to integrate into pipeline (Latest Release- July 2015)
    • Input:VCF, tab-delimted file
    • Output: tab-separated file of annotations
11. AVIA
    • Description: Annotation, Visualization, and Impact Analysis; “The tool is based on coupling a comprehensive annotation pipeline with a flexible visualization method. We leveraged the ANNOVAR (Wang et. al, 2010) framework for assigning functional impact to genomic variations by extending its list of reference annotation databases (RefSeq, UCSC, SIFT, Polyphen etc.) with additional in-house developed sources (Non-B DB, PolyBrowse).”
    • Input: BED
    • Output: Table of annotations with gene annotation features
12. BioR
    • Description: (Mayo Clinic) (Page last updated June 2015) Biological Reference Repository; “data integration tool that enables coordinate based searches and joins based on strings”; “BioR consists of two parts 1) the BioR toolkit which depends on Java…. 2) the BioR catalogs which are the data files used by the system”
    • Input: VCF
    • BioR-Supported Catalogs (tar-gzip files): dbSNP, 1000 genomes, HapMap, OMIM, NCBIGene
    • Output: VCF + JSON
13. CADD
    • Description: Combined Annotation Dependent Depletion; tool for scoring SNV deletions/insertions; “integrates multiple annotations into one metric”; Score strongly correlates with allelic diversity and pathogenicity; links to 1000 Genome variants; uses Ensembl Variant Effect Predictor
    • Input: VCF
    • Output: CADD score
14. CandiSNPer
    • Description: web application, characterizes SNPs located in vicinity of SNP of interest;
    • Input: enter SNP ID (rsID), choose population, region, measure for LD, threshold plot format, color of SNPs, and chose to show genes
    • Output: Imagefile
15. CanvasDB
    • Description: “local database infrastructure for analysis of targeted- and whole genome re-sequencing projects”; dependent on MySQL, R, and ANNOVAR
    • Input:
    • Output:
16. CAROL
    • Description: (Wellcome Trust Sanger); Combined Annotation scoRing toOL; Combined functional annotation score of nonsynonymous coding variants; Combines information from PolyPhen-2 and SIFT
    • Input: tab-delimited with columns obtained from PolyPhen-2 and SIFT output
    • Output: tab-delimited file
17. CHASM
    • Description: Cancer-specific High-throughput Annotation of Somatic Mutations; Last updated May 2014; uses Random Forest Method to “distinguish between driver and passenger somatic mutations”; Positive driver class curated from COSMIC database; packed together with SNVBox (database)
    • Input:Passenger mutation rates, Transcript and amino acid change, Genomic coordinates
    • Output: CHASM score, p-value, FDR
18. CRAVAT
    • Description: Cancer-Related Analysis of Variants Toolkit; Web application; Uses CHASM, VEST, SNVGet; “CRAVAT provides predictive scores for germline variants, somatic mutations and relative gene importance, as well as annotations from published literature and databases” Latest Release May 2015;
    • Input: VCF, CRAVAT format
    • Output: CRAVAT report- MS Excel spreadsheet or tab-separated file (emailed)
19. CUPSAT
    • Description: Cologne University Protein Stability Analysis Tool; “tool to predict changes in protein stability upon point mutations”; web service program; Can predict mutant stability from existing PDB structures or custom protein structures
    • Input:for PDB- provide PDB ID and Amino Acid Residue Number; for custom- PDB file format
    • Output:
20. DANN
    • Description: Deleterious Annotation of genetic variants; standalone program, uses “the same feature set and training data as CADD to train a deep neural network”; can catch nonlinear relationships; “There are four different datasets: training, validation, testing, and ClinVar_ESP...The ClinVar_ESP dataset is also a testing set containing a set of “gold standard” pathogenic and benign variants”
    • Input:
    • Output:
21. ESEfinder
    • Description: Exonic Splicing Enhancer; useful for interpretation of point mutations/polymorphisms that are disease-associated; GUI interface; web app program
    • Input: FASTA
    • Output: html or plain text format, graphical display of results
22. Exomiser
    • Description: Wellcome Trust Sanger; functionally annotates variants from whole-exome sequencing data; Based on Jannovar and uses UCSC KnownGene; Java program; web app program (Page last modified Feb 2015)
    • Input: VCF
    • Output: TSV, VCF
23. FamAn
    • Description: Automated variant annotation pipeline for family-based sequencing studies; Annotaties SNVs and INDELs; 4 models- autosomal dominant, autosomal recessive, de novo mutations and a general model; “A variety of annotations are provided for each segregating variant: number of family (and family ID) each variant hits, variant genomic location and coding effect (based on snpEff), loss-of-function mutation annotation, selected ENCODE annotation, allele frequency in the 1000 Genomes Project, allele frequency in the Exome Variant Server (ESP6500), segmental duplication annotation, SIFT, PolyPhen2, LRT, MutationTaster, GERP++, PhyloP, SiPhy, etc.” (Last updated May 2014)
    • Input: VCF
    • Output: two excel compatible outputs
24. GeneTalk
    • Description: Combines tool for filtering and data analysis with an online network for genetic professionals; Different degrees- basic license, premium license, in-house solution (the last ones are paid for- Commercial tool?)
    • Input: VCF
    • Output: GeneTalk Annotation- includes clinical data, medical relevance, scientific relevance (http://www.gene-talk.de/public/GeneTalk_Whitepaper_Annotations.pdf)
25. GeneVetter
    • Description: “GeneVetter is a tool designed for investigation of the background prevalence of exonic variation in the Phase 3 1000 Genomes data under user defined filtering criteria”; web app program; GeneVetter uses GRch37p4 (hs37d5.fa.gz), dbSNP build 138, 1000G Phase 3, clinvar_2014072
    • Input: VCF
    • Output: TIMS score, summary table, PCA plot
26. GSITIC
    • Description: (Broad Institute) Last update- July 2014; Identifies genomic regions that are significantly “amplified or deleted”; Each is given a G score; gives genomic locations and q-values from aberrant regions
    • Input: segmentation file -seg, markers file -mk (required); -array file list -alf, CNV file -cnv
    • Reference genome: -refgene (created in MATLAB, GISITIC provides four reference genomes: hg16.mat, hg17.mat, hg18.mat, hg19.mat
    • Output: All lesions file (text file), amplifications file (text file), deletion genes file (text file), Gistic Scores file, Segmented copy number (pdf file), amplification score GISTIC plot (pdf file), Deletion score/q-vale GISTIC plot (pdf file)
27. HOPE
    • Description: Have yOur Protein Explained; Web app program; Automatic mutant analysis server that provides structural effects of a mutation; Uses BLAST against UniProt and PDB along with homology modeling
    • Input: FASTA protein sequence, or accession code of protein of interest
    • Output: a report containing information from a “decision tree” and illustrated figures and animations
28. Human Splicing Finder
    • Description: Last update: May 2013; aimed to help study pre-mRNA splicing; combines 12 algorithms to identify mutations’ effect on splicing motifs; uses ensembl database 70
    • Input: Gene Name, Ensembl transcript ID, Ensembl Gene ID, Consensus CDS, RefSeq Peptide ID, or own sequence (looks like you can enter FASTA)
    • Output: Chart with columns for predicted signal, predicted algorithm, cDNA position and interpretation
29. LARVA
    • Description: Large-scale Analysis of Variants in noncoding Annotations; New version released July 2015; Command-line program; used for studying noncoding variants; integrates comprehensive set of noncoding elements, modeling their mutation count; Dependent on C++ and BEDtools
    • Input: multiple
    • Output:
30. LINKAGE
    • Description:three main programs: mlink (calculates lod scores at fixed values for the recombination fraction in one interval of a genetic map), linkmap (calculates location scores for positions of a disease locus along a marker), and ilink (estimates parameters including recombination fractions, allele frequencies, penetrances, etc)
    • Input: pedfile (processed by MAKEPED) and datafile (reflects loci for each individual; set in PREPLINK)
    • Output:
31. MAC
    • Description: MNV Annotation Corrector; Ad hoc software, fixes incorrect amino acid predictions that are caused by multiple nucleotide variations; Uses existing annotators ANNOVAR, SnpEff, VEP (last update April 2015) (only 1 download this week → not popular)
    • Input: List of called SNVs and corresponding BAM
    • Output: Report identifying block of mutation within codon (BMCs)
32. mit-o-matic
    • Description: focuses on mtDNA, provides clinically relevant information from different resources; two component pipeline: command link for alignment of NGS reads and online version that provides genetic report on mitocondrial variants
    • Input:FASTQ, pileup
    • Reference sequence: rCRSm
    • Output: Online version gives comprehensive genetic report
33. Mutadelic
    • Description: Web App program; “This application generates reports on inherited mutations in five genes (ANK1, SLC4A1, SPTA1, SPTB and EPB42) associated with the following rare Mendelian blood disorders: Hereditary Spherocytosis (HS), Hereditary Elliptocytosis (HE) and Hereditary Pyropoikilocytosis”; Newer program- recently validated on omictools
    • Input: Can upload coordinates of DNA variants or VEP
    • Output: Displayed on web or can be downloaded in Excel or RDF format
34. MutationTaster
    • Description: (Last post on site 2014) Web app program; Rapid evaluation of disease causing alterations; uses NCBI 37 and Ensembl 69
    • Input: HGNC symbol, NCBI GeneID, or Ensembl ID,
    • Output: Report containing prediction, summary, name of alteration, etc
35. MutPred
    • Description: web app tool; Classifies amino acids substituation as disease associated or neutral in humans; Last modified Feb. 2014; Based on SIFT, trained using Human Gene Mutation Database
    • Input:
    • Output: “The output of MutPred contains a general score (g), i.e., the probability that the amino acid substitution is deleterious/disease-associated, and top 5 property scores (p), where p is the P-value that certain structural and functional properties are impacted.”
36. MutSigCV
    • Description: (Broad Institute) Mutation Significance (CV= covariates); Analyzes mutations discovered in DNA sequencing to identify genes that were mutated more often than expected
    • Input: mutations.maf, coverage.txt, covariates.txt
    • Output: output.txt
37. NGS-SNP
    • Description: Collection of command-line scripts for providing rich SNP annotations; “NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts and proteins when applicable”;
    • Input: Samtools consensus pileup, Maq, diBayes, Genetic format, VCF
    • Output: File containing annotated SNPs is copied from SNP list and some classes are added
38. Oncotator
    • Description: (Broad Institute) “Tool for annotating human genomic point mutations and data relevant to cancer researchers”; Web app; Supports annotation of data from ClinVar, dbSNP, 1000 genomes (plus many other external sites); Only GRCh27 coordinates supported; Last update: April 2015
    • Input: tal-delimited file
    • Output: tab-delimited MAF
39. PANTHER
    • Description: Protein ANalysis THrough Evolutionary Relationships; Web app program, also has its own database; Classification system used to classify proteins and their genes; Also, “Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein”; Updated in 2015
    • Input: Data from PANTHER, IDs from Ensembl, EntrezGene, NCBI GI numbers, NCBI UniGene IDs HUGO, UniProt; if ID type is not one of the above, can input txt file or excel format
    • Output: Analysis results displayed online
40. PESX
    • Description: Putative Exonic Splicing Enhancers/Silencers; (Can’t tell if this is outdated or not)
    • Input: FASTA or plain text
    • Output: Excel spread sheet
41. Phen-Gen
    • Description: Combines patient's’ disease symptoms with sequencing data; Standalone or Web app version; Only excepts 1 family per run, in order to evaluate unrelated individuals, each sample needs to be run individually
    • Input: Variant- VCF; Pheotype- HPO; Pedigree- PED
    • Output: Combined scores file, variants for top genes file
42. PMUT
    • Description: Aimed at annotation and prediction of pathological mutations; based on different kinds of sequence info and neural networks to process information
    • Input: FASTA
    • Output; Simple yes/no and reliability index
43. PROVEAN
    • Description: Protein Variation Effect Analyzer; predicts whether an amino acid substitution or indel has impact on biological function of the protein; “comparable to SIFT or Polyphen-2”; Standalone, Web app, Command line or GUI; Last update May 2014
    • Input: FASTA, list of variants;
    • Output: tab-separated columns including Variant, Provean Score and prediciton
44. Rescue-ESE
    • Description: “An online tool for identifying candidate ESEs in vertebrate exons”; Web application; For human, mouse, zebrafish, pufferfish
    • Input: multi-FASTA or plain text
    • Output:
45. SCAN
    • Description: Web application program, includes a database as well; Database contains physical-based SNP annotations and functional annotations; “Information on physical, functional, and LD annotation served on the SCAN database comes directly from public resources, including the HapMap (release 23a), NCBI (dbSNP 129), or is information created by us using data downloaded from these public resources”; “SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms”
    • Input:
    • Output: HTML, comma-delimited, tab-delimited
46. SeattleSeq Annotation
    • Description: “SeattleSeqAnnotation137 was most recently updated October 13, 2013. The current version is 8.08. The most recent site, based on dbSNP build 141, and hg38/NCBI 38”; Provides annotations for SNVs and Indels- includes dbSNP rsID, gene names and accession numbers, variation functions, protein positions and amino acid changes, conservation scores, HapMap frequencies, PolyPhen predictions and clinical association.
    • Input: Maq, gff, CASAVA, VCF, GATK bed, custom
    • Output: “default output file format is a header line (starting with "#") followed by tab-separated annotations”; VCF
47. seqminer 3.7
    • Description: “Efficiently Read Sequence Data (VCF Format, BCF Format and METAL Format) into R”; Command line package program; Published August 2015
    • Input: VCF, BCF
    • Output: VCF
48. SG Adviser
    • Description: Scripps Genome Annotation and Distributed Variant Interpretation Server, web developed applications for variant annotation, “Downstream applications of variant annotation include: Clinical sequencing applications including: carrier testing, or identification of causal variants in molecular diagnosis, tumor sequencing, or diagnostic odyssey. Prioritization of variants prior to statistical analysis of sequence based disease association studies, especially for automated set-generation and enrichment of likely functional variants within sets. Identification of causal variants in post-GWAS/linkage sequencing studies. Identification of causal variants in forward genetic screens (stay tuned for non-human annotation)”
    • Input: SNV- VCF, BED, and a few others; CNV- BED, CNVator, plus others
    • Output: tab-delimited file
49. SNAP-2
    • Descriptio

 UPARSE >
OTU clustering for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. UCHIME >
Chimeric sequence detection. PILER >
De novo genome repeat finder. PILER-CR >
Detection of CRISPR repeats in bacterial genomes. QSCORE >
Compare two multiple alignments for benchmarking. PALS >
Whole-genome alignment. PREFAB >
Protein Reference Alignment Database. MSA benchmark collection >
Selected multiple alignment benchmarks in a standardized FASTA format.

Address of the bookmark: http://drive5.com/software.html

Job Qualifications
Education and Experience
• Master Degree in Bioinformatics, Computational biology, Scientific Computing or related field
• 3-5 years of Post-Master’s experience in Bioinformatics software development
• Proven experience developing high throughput bioinformatics applications
Required Competencies
• Strong proven experience in Python programming language in Linux environment
• Proven High Performance computing experience (LSF/SGE/OGE)
• Exposure in code versioning and repository management (GIT/SVN)
• Proven experience in Bioinformatics algorithm development
• Deep understanding in Bioinformatics tools, data types
Desired Competencies
• Familiarity working in a scientific computing environment (NumPy, SciPy, Pandas etc.)
• Familiarity working with Cloud technologies (AWS, Azure)
• Ability to demonstrate solid analytical skills and exceptional attention to detail.
• Experience in relational databases and data structures
• Proven experience working with teams using agile software development methodologies and processes
• Familiarity with Service Oriented Architecture (SOA)
• Familiarity with build tools (Jenkins, make, ANT, Maven)
• Exposure to project management tools (JIRA, Confluence, RED MINE, etc.)

More at http://careers.dupont.com/jobsearch/job-details/senior-bioinformatics-software-developer/012939W-01/

AutoDock

Stochastic (GA)

Flexible ligand and partially flexible target

ArgusLab

Systematic

Flexible ligandX-Score based

DOCK

Systematic (IC)

Flexible ligandDOCK 3.5 (force field)

eHITS

Systematic (RBD of fragments followed by reconstruction)Flexible ligand and partially flexible targetHiTS_Score (empirical)

FlexX

Systematic (IC)Flexible ligandFlexX SF (empirical)Commercial

FLIPDock

Stochastic (GA)Flexible ligand and flexible targetAUTODOCK (empirical)

FRED

Systematic (RBD)Flexible ligandChemScore, PLP, ScreenScore, ChemGauss (empirical/consensus)

GOLD

Stochastic (GA)

Flexible ligand and partially flexible targetGoldScore, ChemScore (empirical), ASP (knowledge based)

ICM

Stochastic (MC)

Flexible ligand and partially flexible targetICM SF (empirical)

ParDOCK

Stochastic (MC)

RigidBAPPL (empirical)

PLANTS

Stochastic (ACO)Flexible ligand and partially flexible target

CHEMPLP, PLP (empirical)

Surflex

Systematic (IC/MA)Flexible ligandHammerhead based (empirical)

Point to note:

Several studies have shown that the performance of most docking tools is highly dependent on the particular characteristics of both the binding site and the ligand to be investigated, and the determination which method would be more suitable in a specific context is difficult. We encouraged you to check several docking methods to determine which one(s) work best for your system.

Address of the bookmark: https://github.com/PapenfussLab/gridss

• major/MySQLTuner-perl - MySQLTuner is a script written in Perl that will assist you with your MySQL configuration and make recommendations for increased performance and stability.
• kraih/mojo - Mojolicious - Perl real-time web framework
• petdance/ack2 - ack 2.0 is a greplike tool optimized for programmers searching large heterogeneous trees of source code.
• rsnapshot/rsnapshot - a tool for backing up your data using rsync (if you want to get help, use https://lists.sourceforge.net/lists/listinfo/rsnapshot-discuss)
• fletcher/MultiMarkdown - Expanded perl version of John Gruber's original Markdown --- No longer under active development since MMD 3
• PerlDancer/Dancer - The easiest way to write web applications with Perl (Perl web micro-framework)
• duckduckgo/zeroclickinfo-goodies - DuckDuckGo Instant Answers based on Perl & JavaScript
• sjdy521/Mojo-Webqq - 使用Perl语言（不会没关系）编写的smartqq/webqq客户端框架（非GUI），可通过插件提供基于HTTP协议的api接口供其他语言或系统调用
• chromatic/modern_perl_book - Modern Perl: the book
• gugod/App-perlbrew - Manage perl installations in your $HOME
• muennich/urxvt-perls - Perl extensions for the rxvt-unicode terminal emulator
• sjdy521/Mojo-Weixin - 使用Perl语言（不会没关系）编写的微信/weixin/wechat客户端框架（非GUI），可通过插件提供基于HTTP协议的api接口供其他语言或系统调用
• Nordaaker/convos - Better group chat
• mikaku/Monitorix - Monitorix is a free, open source, lightweight system monitoring tool.
• vsespb/mt-aws-glacier - Perl Multithreaded Multipart sync to Amazon Glacier
• skx/sysadmin-util - Tools for Linux/Unix sysadmins.
• perl-carton/carton - Bundler or pip freeze for Perl
• PerlDancer/Dancer2 - Perl Dancer Next Generation (rewrite of Perl Dancer)
• OpenKore/openkore - A free/open source client and automation tool for Ragnarok Online
• hachiojipm/awesome-perl - A curated list of awesome Perl frameworks and libraries. Come on Pull Requests!
• Perl/perl5 - The Perl 5 language interpreter (MIRROR ONLY)
• fglock/Perlito - Perl 5 and Perl 6 compilers
• miyagawa/Starman - Starman is a high-performance preforking Perl PSGI web server
• ronilaukkarinen/weed - Heavily Xchat inspired beautiful irssi theme.
• trizen/youtube-viewer - A lightweight application for searching and streaming videos from YouTube.
• rakudo/star - Rakudo Star Perl 6 distribution
• GouveaHeitor/nipe - Nipe is a script to make Tor Network your default gateway.
• yuvi/gas-preprocessor - Perl script that implements a subset of the GNU as preprocessor that Apple's as doesn't
• mongodb/mongo-perl-driver - Perl driver for the MongoDB
• wireghoul/dotdotpwn - DotDotPwn - The Directory Traversal Fuzzer
• oysttyer/oysttyer - An interactive console text-based command-line Twitter client written in Perl
• bioperl/bioperl-live - Core BioPerl 1.x code
• tadzik/rakudobrew - Perl 6 installation manager
• fwaeytens/dnsenum - dnsenum is a perl script that enumerates DNS information
• evalEmpire/perl5i - A single module to fix as much of Perl 5 as possible in one go
• shirkdog/pulledpork - Pulled Pork for Snort and Suricata rule management (from Google code)
• hollie/misterhouse - Perl open source home automation program. It's fun, it's free, and it's entirely geeky.
• stevan/p5-mop-redux - A(nother) MOP for Perl 5
• stevan/p5-mop-original - A MOP for Perl 5
• pgbackrest/pgbackrest - Reliable PostgreSQL Backup & Restore
• gempesaw/Selenium-Remote-Driver - Perl Bindings to the Selenium Webdriver server
• libwww-perl/libwww-perl - The libwww-perl collection is a set of Perl modules which provides a simple and consistent application programming interface to the World-Wide Web. The main focus of the library is to provide classes and functions that allow you to write WWW clients. The library also contain modules that are of more general use and even classes that help you implement simple HTTP servers.
• andk/pause - Perl authors upload server
• miyagawa/remedie - perl based pluggable media center application
• mojomojo/mojomojo - A Catalyst & DBIx::Class powered Wiki.
• xslate/p5-Text-Xslate - Scalable template engine for Perl5
• moose/Moose - Official repository for Moose
• llaera/slowloris.pl - A new DOS Perl Programm
• colorgcc/colorgcc - colorgcc is a perl script to colorize gcc output. I'm collecting random patches and changes
• bbusschots/hsxkpasswd - A Perl module and terminal command for generating secure memorable passwords inspired by the fabulous XKCD web comic and Steve Gibson's Password Hay Stacks. This is the library that powers www.xkpasswd.net
• Test-More/test-more - Test2, Test::More, Test::Simple and Test::Builder Perl modules for writing tests
• smtpd/qpsmtpd - qpsmtpd is a flexible smtpd daemon written in Perl
• perseo22/pacmanager - Perl/GTK Gnome SSH GUI on steroids. Configure SSH/Telnet connections: users, passwords, EXPECT regular expressions, macros, ...
• noxxi/p5-ssl-tools - various standalone perl scripts
• chromatic/little_plack_book - Using Plack and PSGI in Modern Perl Web Applications
• mschilli/log4perl - Log4j Implementation For Perl
• centreon/centreon-plugins - Collection of plugins for softwares compatible with Nagios plugins
• fayland/perl-net-github - Perl interface to GitHub
• Perl-Critic/Perl-Critic - The leading static analyzer for Perl. Configurable, extensible, powerful.
• abw/Template2 - Perl Template Toolkit v2
• stf-storage/stf - STF - Distributed Object Storage (Perl/MySQL/(Q4M|TheSchwartz|Resque|Redis)/Memcached)
• PerlRedis/perl-redis - Perl binding for Redis database
• pplu/aws-sdk-perl - A community AWS SDK for Perl Programmers
• sveinbjornt/Data-URL-Toolkit - Various tools for working with Data URLs, incl. web application (http://dataurl.net), Mac OS X GUI app, command line tool, Perl modules and Apache module.
• perl6/ecosystem - Perl 6 ecosystem -- modules and more
• moznion/Perl-Lint - Yet Another Perl Source Code Linter
• briandfoy/PerlPowerTools - Perl Power Tools
• gshank/html-formhandler - a Perl Moose HTML form handler
• mskcc/vcf2maf - Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
• miyagawa/web-scraper - Perl web scraping toolkit
• semifor/Net-Twitter - A Perl interface to the Twitter APIs
• kraih/minion - Perl job queue
• fletcher/MultiMarkdown-CMS - Package to assist with publishing a web site using MMD and a few perl scripts
• rcaputo/poe - POE is a portable perl multitasking and networking framework for any event loop.
• kraih/mango - Pure-Perl non-blocking I/O MongoDB driver
• dreamwidth/dw-free - Dreamwidth's open source repository
• garu/Data-Printer - colored pretty-print of Perl data structures and objects
• PerlGameDev/SDL - Rehashing the old perl SDL binding on cpan.org
• yanick/Template-Mustache - Drawing Mustaches on Perl, for fun and profit
• pjcj/Devel--Cover - Code coverage metrics for Perl
• sebthebert/Octopussy - Octopussy - Open Source Log Management Solution
• gphat/chart-clicker - Extensible, Beautiful Charts for Perl
• audreyt/lingua-sinica-perlyuyan - Perl in Classical Chinese in Perl
• book/perlsecret - The perl secret operators
• OCSInventory-NG/OCSInventory-Server - Communication server of OCS Inventory
• jmapio/jmap-perl - JMAP Proxy implemented in Perl
• fusioninventory/fusioninventory-agent - FusionInventory Agent
• samm-git/jvpn - Perl script to connect to the Juniper VPN with Host Checker enabled
• perl11/cperl - a perl5 with classes, types, compilable, company friendly, security
• kbh3rd/shptosvg - Shapefile to SVG renderer in Perl
• famzah/langs-performance - C++ vs. Python vs. Perl vs. PHP vs. Java vs. NodeJS vs. Go vs. Ruby performance benchmark
• agentzh/old-openresty - Obsolete 1st generation of OpenResty written mostly in Perl. Please check out the new OpenResty based on Nginx and Lua instead.
• kraih/mojo-pg - Mojolicious PostgreSQL
• jmcnamara/excel-writer-xlsx - Perl module to create Excel XLSX files.
• plainblack/webgui - A free open source content management system and web application framework. The most widely deployed mod_perl application on the planet.
• mharsch/arcstat - uses Perl to extract, format, and display kstats from the ZFS ARC
• thaljef/Pinto - Curate your own repository of Perl modules
• rcaputo/reflex - Reflex is a class library for writing reactive Perl programs. It provides base classes for reactive objects, and specific subclasses for various tasks.
• memowe/contenticious - A simple file based "CMS" on Mojo steroids!
• rjust/defects4j - A Database of Existing Faults to Enable Controlled Testing Studies for Java
• elastic/elasticsearch-perl - New Perl low-level client
• blogs-perl-org/blogs.perl.org - Templates and stuff for the blogs.perl.org web site
• agordon/dancer_bootstrap_fontawesome_template - A template for quick-starting applications using Perl's Dancer, Twitter's Bootstrap and Font-Awesome.
• fletcher/SimplenoteSync - perl routine to sync folder of text files with your notes on Simplenote
• tobert/perl-ssh-tools - A more capable DSH / cluster ssh suite
• skx/dhcp.io - Dynamic DNS - Via Redis, Perl, and Amazon Route53.
• perl6/mu - Universal Perl 6 repository (formerly called "pugs repository")
• perl5-dbi/dbi - DBI - The Perl 5 Database Interface
• masterzen/mysql-snmp - Net-SNMP perl agent for monitoring MySQL servers
• rizen/Facebook-Graph - A perl module to help navigate the intricacies of the Facebook Graph API.
• lhost/sendxmpp - perl-script to send xmpp (jabber), similar to what mail(1) does for mail.
• Real-Gecko/Filemin - File manager for Webmin written completely in perl
• preaction/Statocles - Static website CMS
• jonswar/perl-mason - Mason 2
• davorg/perlwebbook - A book. About Perl. And the Web.
• plu/Pithub - Perl Github v3 API
• motemen/Wight - Communicate with PhantomJS in Perl (Capybara+Poltergeist to Perl)
• ingydotnet/pegex-pm - Pegex Parser for Perl
• ewels/ClusterFlow - A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
• denny/ShinyCMS - ShinyCMS is an open source CMS built in Perl using the Catalyst framework.
• nassosoassos/sail_align - SailAlign is an open-source software toolkit for robust long speech-text alignment implementing an adaptive, iterative speech recognition and text alignment scheme that allows for the processing of very long (and possibly noisy) audio and is robust to transcription errors. It is mainly written as a perl library but its functionality also depends on freely available software, namely HTK, srilm and sclite.
• masak/web - A Perl 6 web framework
• agentzh/perl-systemtap-toolkit - Real-time analyzing and diagnosing tools for perl 5 based on SystemTap
• vti/showmethedesktop - Perl + VNC + WebSockets + HTML5 Canvas
• vmbrasseur/Perl_Companies - A list of companies which use Perl. Initially generated from postings to jobs.perl.org.
• perlorg/perlweb - Various perl.org websites
• norbu09/Net--Dropbox - perl interface to the Dropbox API
• line/line-bot-sdk-perl - LINE::Bot::API - SDK of the LINE Messaging API for Perl
• ericblue/Perl-FitBit-API - Provides an OO API for fetching fitness data from fitbit.com. Currently there is no official API, however data is retrieved using XML feeds that populate the flash-based charts.
• ericblue/Perl-Belkin-WeMo-API - Perl-Belkin-WeMo-API
• EnlightenedPerlOrganisation/task-kensho - A Glimpse at an Enlightned Perl Distribution
• dasdom/CreateAppStoreBill - A perl script and tex files to create bills for the German tax office from Apple's financial reports.
• plicease/FFI-Platypus - Write Perl bindings to non-Perl libraries with FFI. No XS required.
• ido50/Svsh - Process supervision shell for daemontools, perp, s6 and runit
• skx/templer - A modular extensible static-site-generator written in perl.
• lestrrat/p5-ZMQ - libzmq Perl binding
• jpoliv/wakeonlan - Perl script for waking up computers via Wake-On-LAN magic packets
• dod38fr/config-model - Perl module to create configuration editor wtih semantic validation
• pjlsergeant/test-bdd-cucumber-perl - Test::BDD::Cucumber - Cucumber in Perl
• onishi/perl5-devel-kytprof - Devel::KYTProf - Simple Perl code profiler
• finance-quote/finance-quote - Finance::Quote module for Perl
• fcuny/net-http-spore - Perl implementation for SPORE
• dpavlin/perl-cwmp - Perl ACS server implementing CWMP protocol to manage CPE clients
• abh/pgeodns - Geographic Perl Nameserver
• timbunce/devel-nytprof - Perl Devel::NYTProf
• symkat/Daemon-Control - Daemon::Control - Create init scripts in Perl
• sartak/webmachine-perl - A Perl port of Webmachine
• rhuss/jmx4perl - JMX access tools and modules
• Perl/docker-perl - Dockerfiles for index.docker.io (official Perl Docker image)
• duckduckgo/p5-app-duckpan - DuckDuckHack OpenSource Development Application
• CaptTofu/DBD-mysql - DBD::mysql Perl client driver for the MySQL and MariaDB databases
• beide/Bootimg-scripts - Perl scripts for unpacking and repackaging Android boot.img's. I did not write these, just sharing.
• spezifanta/SteamCalculator-Scripts - Perl scripts, which parses the Valve's Steam store.
• rurban/perl-compiler - B::C - Moved over from googlecode
• pkrumins/perl-tcp-proxy - A simple TCP proxy written in Perl. Uses IO::Socket::INET and IO::Select for multiplexing.
• perl-users-jp/perl-advent-calendar - japanese perl advent calendar - fork 禁止
• Perl-Toolchain-Gang/ExtUtils-MakeMaker - Perl module to make Makefiles and build modules (what backs Makefile.PL)
• msgpack/msgpack-perl - MessagePack serializer implementation for Perl / msgpack.org[Perl]
• kablamo/git-spark - Plot your commit history on the command line with sparklines. A mash up of git and spark and Perl.
• Aralhach/bashobfus - A small bash minifier/obfuscator written in Perl.
• aesuli/Amazon-downloader - Two perl scripts to download and parse Amazon's reviews
• sjdy521/pfqq - 【该项目已停止维护，请关注重构项目: Mojo-Webqq】使用Perl语言编写的webqq客户端框架（非GUI），支持旧版webqq的多重md5带盐登录密码算法以及新版smartqq的md5+rsa+tea+base64组合登录密码算法
• raszi/colorize - Log colorizer perl script
• iinteractive/OX - the hardest working two letters in Perl
• ap/perldoc-complete - A bash completion helper for perldoc
• xsawyerx/perl-android-scripts - Collection of Perl scripts (examples, programs) that run on Android using ASE
• typester/kamaitachi - perl flash media server
• szabgab/perlmaven.com - The source files of the Perl Maven articles
• petdance/perl101 - The source for perl101.org
• acme/git-pureperl - A Pure Perl interface to Git repositories
• vti/text-haml - Haml parser in Perl
• jploski/epic-ide - EPIC - Eclipse Perl Integration (new official repository!)
• jnthn/blizkost - Makes Perl 5 available as if it were just another Parrot language by embedding the Perl 5 interpreter.
• jeroennijhof/pam_script - PAM script module will allow you to execute scripts during authorization, password changes and sessions. This is very handy if your current security application has no pam support but is accessable with perl or other scripts.
• jberger/Zoidberg - A modular perl shell
• hitode909/App-PRT - Command line tool for Perl code refactoring
• fluent/fluent-logger-perl - A structured logger for Fluentd (Perl)
• dann/p5-cpan-packager - CPAN::Packager is a tool to help you make packages from perl modules on CPAN.
• cotto/www-workflowy - unofficial reverse-engineered Perl 5 interface to Workflowy
• Corion/www-mechanize-firefox - The API of WWW::Mechanize, combined with the Javascript-power of Firefox
• cooldaemon/RabbitFoot - An asynchronous and multi channel Perl AMQP client. It uses Coro and AnyEvent::RabbitMQ.
• perlpilot/perl6-docs - Documents relating to Perl 6
• ingydotnet/mo-pm - Perl Micro Objects
• gnp/psh - Perl Shell (psh) — Aspiring to be your primary login shell
• comewalk/google-api-perl-client - Google APIs Client Library for Perl
• CiderWebmail/CiderWebmail - Perl/Catalyst/AJAX based Webmail
• barbie/perl-jam - Perl Jam - a book about organising conferences
• typester/perldojo - online perl testing!
• tsee/ZeroMQ-Perl - Perl interface to 0MQ2
• trizen/obmenu-generator - A fast menu generator for the Openbox Window Manager.
• rjbs/App-Cmd - perl framework for testable, extensible command line apps
• grampajoe/Autodatamosh - Perl script that automatically datamoshes MPEG4-encoded AVI videos.
• xtaran/unburden-home-dir - Automatically unburden $HOME from caches, etc. Useful for $HOME on SSDs, small disks or slow NFS homes. Can be triggered via an hook in /etc/X11/Xsession.d/.
• rjbs/Email-Sender - a perl library for sending email
• kruser/atbat-mongodb - A Perl project that pulls data from MLB's AtBat servers and shoves them into a local MongoDB
• jonswar/perl-chi - Perl CHI distribution
• andrewcmyers/civs - Condorcet Internet Voting System
• sjdy521/Mojo-SinaWeibo - 使用Perl语言编写的新浪微博客户端SDK，通过微博私信和微软小冰进行问答，提供小冰API接口，其他微博功能敬请期待
• perigrin/blawd - Simple Blogging Software in Perl, similar to blosxome or Jekyll
• jacquesg/p5-Git-Raw - Perl bindings to the Git linkable library (libgit2)
• ingydotnet/io-all-pm - All in One Perl IO
• dagolden/Capture-Tiny - (Perl) Capture STDOUT and STDERR from Perl, XS or external programs
• beppu/squatting - A Camping-inspired Web Microframework for Perl
• tempire/perl-google-voice - Perl module to interact with Google::Voice
• njh/perl-net-sdp - Perl Module : Session Description Protocol (rfc2327)
• songzan/perl5-doc - Perldoc Help Chinese Planning
• sisimai/p5-Sisimai - Mail Analyzing Interface for email bounce: A Perl module to parse RFC5322 bounce mails and generating structured data as JSON from parsed results. Formerly known as bounceHammer 4: an error mail analyzer.
• shenwei356/bio_scripts - Practical, reusable scripts for bioinformatics
• mozilla-bteam/bmo - bugzilla.mozilla.org source
• jamadam/mojo-legacy - mojo for Perl-5.8.7
• briandfoy/Learning-Perl-Sample-Files - Extra files for use with Learning Perl
• theory/uri-db - Perl module representing database URIs
• semifor/twirc - Twitter / IRC gateway in perl
• makamaka/JSON - perl implementation of JSON encoder/decoder
• lukec/cpan-selenium-rc-perl - Test-WWW-Selenium Perl Selenium RC Driver
• keeth/Net-OAuth2 - OAuth 2.0 for Perl
• wireghoul/doona - Fork of Bruteforce Exploit Detector
• pjf/autodie - Make functions succeed or die in Perl, with lexical scope.
• PDLPorters/pdl - Scientific computing with Perl
• ewaters/net-amqp - Implementation of the AMQ Protocol in Perl
• demanuel/NewsUP - NewsUP a binary usenet uploader/poster (multiple connections, SSL and NZB).
• ati/ljsm - perl script for LiveJournal blog backup
• vti/underscore-perl - Underscore-perl is a Perl clone of Underscore.js
• techsneeze/dmarcts-report-parser - A Perl based tool to parse DMARC reports from an IMAP mailbox or from the filesystem, and insert the information into a database. ( Formerly known as imap-dmarcts )
• prepan-developers/prepan - Social Reviewing for Perl Modules
• portcullislabs/rdp-sec-check - PERL script to enumerate security settings of an RDP Service (AKA Terminal Services)
• mlawren/githook-perltidy - Run perltidy as a Git pre-commit hook
• miyagawa/xml-atom - XML::Atom perl module
• jric/epubtohtml - A simple perl script to convert epub documents to documents that browsers can natively browse.
• jmcnamara/spreadsheet-writeexcel - Perl module to write Excel binary files
• FormFu/HTML-FormFu - HTML Form Creation, Rendering and Validation Framework. Just define the form, and let FormFu do the all heavy lifting.
• cbbrowne/autodoc - PostgreSQL Autodoc - dumps a Postgres schema in several useful documentary forms
• xen-tools/xen-tools - xen-tools is a collection of simple perl scripts which allow you to easily create new Xen guest domains upon your Xen host server.
• tokuhirom/Test-TCP - Test::TCP for perl
• timbunce/java2perl6 - Parse Java class files and generate corresponding Perl6 Class and Role files
• stoned/pll - Yet another Perl local::lib+cpanm helper script
• stevan/promises-perl - An implementation of Promises in Perl
• oetiker/mrtg - MRTG - Multi Router Traffic Grapher
• monitoring-plugins/monitoring-plugin-perl - Perl module Monitoring::Plugin - Nagios::Plugin
• mirod/xmltwig - XML, the Perl way
• kraih/perl-raptor - Perl 5 Raptor
• KKBOX/mpdnsd-perl - Marco Polo DNS Daemon
• kevinphilp/Perl-gtk3-Tutorial - Some notes on using Gtk3 with Perl
• kesor/p5-cucumber - Cucumber for Perl 5
• Ensembl/ensembl - The Ensembl Core Perl API and SQL schema
• dankogai/p5-encode - Encode - character encodings (for Perl 5.8 or better)
• rocky/Perl-Devel-Trepan - Perl port of trepanning debugger
• rafl/devel-declare - Adding keywords to perl, in perl
• petdance/html-tidy - HTML::Tidy, a Perl wrapper about libtidy
• libwww-perl/URI - The Perl URI module
• leto/math--gsl - Perl interface to the GNU Scientific Library
• jensenja/graphite-snmp-collector - Asynchronous Perl to collect SNMP data to feed into Graphite
• hachi/Perlbal - Perl HTTP Load Balancer
• bucardo/dbdpg - Perl Postgres driver DBD::Pg aka dbdpg
• aki2o/plsense - Omni completion tool for Perl
• zigorou/perl-JSV - JSON Schema implementation for Perl
• worldmind/perlqual - Wrapper for some tests for Perl code quality
• trizen/trizen - Lightweight AUR Package Manager
• tokuhirom/optimize-perl-doc - how to optimize your perl code?
• peterkeen/proclaunch - A pure-perl process management system
• Ovid/DB--Color - Syntax highlighting the Perl debugger
• jpa/Moose-Doc-JA - Perl Moose Documentation In Japanese
• hakobe/Guita - Gist clone for private use written in Perl
• gonzoua/EBook-EPUB - EBook::EPUB perl module for generating EPUB document
• geuma/pDLNA - perl DLNA MediaServer
• dequis/tmux-url-select - Keyboard based URL selector that integrates with tmux
• Blaizer/ModernPerl-sublime - Perl syntax highlighting for Sublime Text that isn't outdated
• aleex42/netapp-cdot-nagios - Nagios-Checks for monitoring NetApp cDOT-Systems via NetApp Perl API
• simmel/urxvt-resize-font - URxvt Perl extension for resizing the font
• pkrumins/social-scraper - Social scraper is a Perl program that scrapes reddit, digg, stumbleupon, delicious, furl, flickr, simpy, boingboing, wired for content that matches the given patterns.
• metomi/fcm - FCM: a modern Fortran build system + wrappers to Subversion for scientific software development
• khrt/Raisin - Raisin - a REST API micro framework for Perl 
• joshua-hull/Reddit-Image-Scraper - Perl script to download imaged hosted at imgur.com linked from a subreddit at reddit.com
• dpavlin/perl-Redis-obsolete - perl binding for Redis database - latest development is in melo's repository
• cho45/Niro - Blogging System for personal use written in Perl.
• acme/net-amazon-s3 - Use the Amazon S3 - Simple Storage Service from Perl
• vti/plack-middleware-socketio - Socket.IO Perl/Plack implementation DEPRECATED USE PocketIO INSTEAD
• textmate/perl.tmbundle - TextMate support for Perl
• sourceperl/mbtget - A simple modbus/TCP client write in pure Perl.
• semifor/net-twitter-lite - A lighter weight (non-Moose) Perl interface to the Twitter API
• kasei/perlrdf - Official releases of RDF::Query may be found on CPAN: http://search.cpan.org/dist/RDF-Query/
• danaj/Math-Prime-Util - Perl (XS) module implementing prime number utilities, including sieves
• AndyA/Test-Harness - Run Perl standard test scripts with statistics
• sni/Monitoring-Livestatus - Livestatus Perl API to access runtime data from Nagios, Icinga and Shinken.
• skx/markdownshare.com - The code behind http://markdownshare.com/
• Perl-Toolchain-Gang/Module-Build - Perl module to configure and build modules (what backs most Build.PLs)
• markstos/CGI--Application - A Perl framework for building reusable web-applications
• lyokato/p5-oauth-lite2 - Perl Library for OAuth 2.0
• KTamas/pflogsumm - postfix stats
• karupanerura/Aniki - The ORM as our great brother.
• jonswar/perl-poet - Perl Poet distribution
• hzhou/MyDef - Programming in the next paradigm -- your way
• houseabsolute/DateTime.pm - A date and time object for Perl
• fayland/perl-lingua-han - all Lingua::Han:: CPAN modules
• eilara/Rx.pl - Microsoft Reactive Extensions clone for Perl
• dams/curses-toolkit - Curses::Toolkit perl module
• adriaandens/fagrant - Vagrant in 100 lines of (Perl) code
• xsawyerx/module-starter - Module::Starter, a tool to help create solid Perl modules from scratch
• Tux/speedtest - Perl CLI for speedtest.net
• tanjiti/perl_tools - perl小工具
• stevan/BreadBoard - Inversion of Control and Dependency Injection for Perl
• salva/p5-Net-OpenSSH - Perl SSH client built on top of OpenSSH
• rudism/NetAuthority - Historical perl code that ran the original NetAuthority.org site
• pssc/squeezy - A command-line utility for controlling squeezebox network audio players via their squeezeserver.
• portcullislabs/udp-proto-scanner - udp-proto-scanner is a Perl script which discovers UDP services by sending triggers to a list of hosts
• perl5-dbi/DBD-mysql - MySQL driver for the Perl5 Database Interface (DBI)
• Ovid/hop - Higher Order Perl modules on the CPAN
• noxxi/p5-io-socket-ssl - IO::Socket::SSL Perl Module
• kingpong/perl-Test-Spec - rSpec-like test system for Perl
• kensanata/oddmuse - A simple wiki engine written in Perl. No database required.
• gugod/Test-Continuous - (Perl) Run your tests suite continusouly when developing.
• grickit/Gambot - Gambot is a modular IRC bot written in Perl.
• grantm/Algorithm-CouponCode - Perl library to generate and validate 'CouponCode' strings
• eserte/bbbike - BBBike
• book/Git-Repository - Perl interface to Git repositories
• tokuhirom/FormValidator-Lite - very lite and fast validation library for perl
• szbalint/WWW--Curl - Perl binding for libcurl
• stevan/p5-MOP - A Meta Object Protocol for Perl 5
• sludin/Protocol-ACME - A perl library that provides a simple interface to writing scripts for cert provisioning with Let's Encrypt.
• rurban/App-perlall - create and work with /usr/local/bin/perl5.*
• Robertof/perl-www-telegram-botapi - Perl implementation of the Telegram Bot API
• ReneNyffenegger/PerlModules - (Very) simple scripts for some Perl modules, intended as copy paste templates.
• Ovid/Role-Basic - Roles in Perl. Nothing else.
• njlg/perl-rethinkdb - A Pure Perl RethinkDB Driver
• naoya/perl-Text-LTSV - Text::LTSV - Labeled Tab Separated Value manipulator
• memcached/perl-Cache-Memcached - Cache::Memcached
• KD8EYF/TRBO-NET - mototrbo perl modules for ARS TMS and LRRP
• holbertonschool/Betty - Holberton-style C code checker written in Perl
• gnustavo/Git-Hooks - Framework for implementing Git (and Gerrit) hooks
• fayland/perl-www-contact - WWW::Contact - Get contacts/addressbook from Web
• do-know/Crypt-LE - Crypt::LE (ZeroSSL project) - Let's Encrypt client and library in Perl for getting free SSL certificates (inc. generating RSA/ECC keys and CSRs). HTTP/DNS verification is supported out of the box, easily extended with plugins.
• briandfoy/cpan-script - (Perl) Interact with CPAN from the command line
• beppu/anyevent-couchdb - a non-blocking CouchDB client for Perl based on jquery.couch.js
• yannk/ControlFreak - a process supervisor in Perl
• typester/object-container-perl - simple object container
• trizen/menutray - An application menu through a GTK+ tray status icon.
• TrackingSoft/Kafka - Perl implementation of Kafka API (official CPAN module)
• sushdm/git_svn_externals - A perl script to clone an SVN repository with externals, using git-svn
• Perl-Toolchain-Gang/Test-Harness - Run Perl standard test scripts with statistics
• openresty/lemplate - OpenResty/Lua template framework implementing Perl's TT2 templating language
• mkjellman/perlcassa - a Perl client for Apache Cassandra
• LudovicRousseau/pcsc-tools - Some tools to be used with smart cards and PC/SC
• liyanage/build-entropy-php - The Perl-based build system used to build the Entropy PHP distribution
• lixmal/keepass4web - An application that serves KeePass database entries on a web frontend
• hakobe/p5-Fiber - Ruby like Fiber on Perl
• gray/webservice-google-reader - Perl interface to the Google Reader API
• fayland/chinese-perl-book - free book in Chinese "Master Perl Today"
• bruceravel/demeter - Process and analyze X-ray Absorption Spectroscopy data using Feff and either Larch or Ifeffit.
• beanz/xpl-perl - Perl modules for the xPL Home Automation Protocol
• atom/language-perl - Perl package for Atom
• ewels/clusterflow - A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
• diegok/resque-perl - Perl port of the original Ruby library. It's intended to work using the same backend to share tasks and be able to manage the system using ruby's resque-server webapp. Resque is a Redis-backed library for creating background jobs, placing them on multiple queues, and processing them later.
• perl6/specs - Perl 6 language design documents
• trizen/sidef - A modern object-oriented programming language, implemented in Perl.
• audreyt/pugs - A Perl 6 Implementation
• jlord/git-it-electron - A Git-it Desktop App (A Node.js app, not Perl as GH suggests)
• PerlGameDev/SDL_Manual - The Manual for writing Games in Perl using SDL. Part of TPF grant.
• franckcuny/net-http-spore - Perl implementation for SPORE
• houseabsolute/webmachine-perl - A Perl port of Webmachine
• willemdh/check_netapp_ontap - Check NetApp Ontap 
• unobe/perl-wfa - Perl's WWW::Facebook::API Module
• vti/sockjs-perl - SockJS Perl Plack/PSGI implementation
• schwern/Sex - Perl teaches the birds and the bees
• rjray/rpc-xml - A Perl implementation of the XML-RPC specification
• naoya/mapreduce-lite - An experimental implementation of MapReduce for perl
• miyagawa/perl-app-builder - Turns your perl script into .app using Platypus
• leejo/CGI.pm - The CGI.pm perl module
• kngenie/ias3upload - simple Perl script for uploading files to Internet Archive through its S3-like interface
• jsober/Reddit-API - Reddit API for perl
• jizhang/perl-virtualenv - Virtual Environment for Perl
• Ensembl/ensembl-compara - The Ensembl Compara Perl API and SQL schema
• drforr/Perl-Mogrify - Transmogrify Perl5 code to Perl6 with a plugin system
• cooldaemon/AnyEvent-RabbitMQ - An asynchronous and multi channel Perl AMQP client.
• braintree/braintree_perl - Braintree Perl library
• yuki-kimoto/gitweblite - Git repository browser. This is gtiweb.cgi clone to modern perl.
• yanick/Vim-X - Write Perl functions within Vim
• typester/sniffer-rtmp-perl - rtmp sniffer framework
• tonycoz/imager - Imager - image manipulation from perl. This is a mirror only, pull requests will be closed without comment if I ever notice them. Please submit patches (or bugs) via bug-Imager [at] rt.cpan.org
• tobeychris/hipchat-room-message-APIv2 - This is a simple perl script that will use Hipchat's API v2 to message a room after passing in the room name, authentication token and a message. Also includes features for selecting the colour, notifying the room, passing in an html message, using a proxy and using API v1 should you so choose.
• sass/perl-libsass - Perl bindings for libsass (CSS::Sass)
• ranguard/text-vcard - Perl package to edit and create vCard(s) (RFC 2426)
• pkrumins/perl-tcp-proxy2 - Program for my "A TCP Proxy in Perl" article
• PeterMartini/go-perl - Linking in Go code via XS
• petdance/test-www-mechanize - Test::WWW::Mechanize, a Perl object for testing web pages
• perl-ldap/perl-ldap - Perl LDAP client library
• ntruchsess/perl-firmata - Perl implementation of the firmata client. Originally authored by Aki Mimoto (amimoto) this repository was transfered to Norbert Truchsess (ntruchsess) in 02/2013. Anybody willing to contribute is very wellcome! Please submitt pull-requests against branch 'dev'
• mtw/Bio-ViennaNGS - A Perl extension and collection of utilities for Next-Generation Sequencing (NGS) data analysis
• masukomi/jsonpath-perl - Perl port of JSONPath
• livedoor/Sledge - ancient Perl Web Application Framework.
• kernevil/libfilesys-smbclient-perl - Zentyal packaging of libfilesys-smbclient-perl
• ironcamel/App-p - Steroids for your perl one-liners. Does that mean steroids for your steroids? Is that even possible?
• genoo/GenOO - A Modern Perl Framework for High Throughput Sequencing analysis
• gbarr/perl-libnet - perl libnet library
• evernote/evernote-sdk-perl - Evernote SDK for Perl
• elmex/Construder - A 3D Game written in Perl - inspired by Minecraft
• dsully/perl-crypt-openssl-x509 - Perl interface to OpenSSL's X509 module.
• davorg/perlanet - Simple Planet Clone in Perl
• cosimo/TicketServer - Flickr-like Ticket Server implemented with Perl + DBI + MySQL
• robin13/mediathekp - Perl clone of Mediathek
• rjbs/Mail-DeliveryStatus-BounceParser - perl library to parse email bounce messages
• rjbs/Email-MIME - perl library for parsing MIME messages
• Perl-Toolchain-Gang/Software-License - perl representation of common software licenses
• Perl-Toolchain-Gang/ExtUtils-CBuilder - Compile and link C code for Perl modules
• nothingmuch/git-site-perl - Hooks to keep site_perl in git
• miyagawa/cpanmetadb-perl - CPANMetaDB in Starman and Plack with Carmel
• maxmind/MaxMind-DB-Writer-perl - Create MaxMind DB database files
• mattn/p5-Growl-Any - perl module that provide any growl application
• LyonsLab/coge - CoGe (Comparative Genomics) Platform
• hirose31/inspect-perl-proc - get %INC and dump into file
• formalin14/Transformer - A translation system for static websites. It is used to translate the perl.org website.
• duncs/perl-nagios-object - A group of modules for parsing a Nagios configuration and representing it as objects in perl.
• cyberisltd/ProxyDetect - Perl script to detect the existence of transparent proxies
• ct/net-twitter - Net::Twitter, perl interface to twitter.com
• CpanelInc/cPanel-PublicAPI - A perl module for interfacing with cPanel's various APIs
• bingos/poe - (perl) portable multitasking and networking framework for Perl (mirror of the svn repository)
• xsawyerx/gitflux - A Perl port of gitflow. Really? Yes, really!
• wehu/CljPerl - CljPerl is a lisp on Perl.
• tomill/Acme-Perlingual - Acme::Perlingual - Convert perl code to php or something.
• TJC/Flickr-API2 - A fork of Flickr::API from Perl's CPAN
• soarpenguin/perl-scripts - useful perl script and snippets of code.
• shogo82148/Redis-Fast - fast perl binding for Redis database
• shlomif/catable - CATAlyst BLog Engine - written by perl cats
• rjbs/Perl-PrereqScanner - scan a set of Perl libraries to figure out prereqs, without loading the code
• reyjrar/DreamCatcher - DNS Monitoring Suite
• petdance/file-next - File::Next, a file finding module for Perl 5
• Perl-Email-Project/Email-Valid - perl library to validate email addresses
• perl6/evalbot - IRC bot for executing Perl 6 code