Prokka – Standalone command line tool, takes just a few minutes per genome. This is the best way to get good quality annotation in a flash, which is particularly useful if you have loads of genomes or need to annotate a pangenome or metagenome. Note however that the quality of functional information is not as good as RAST, and you will need several extra steps if you want to do functional profiling and pathway analysis of your genome(s)… which is in-built in RAST.

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

PGAP: NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume.  NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

BEACON (automated tool for Bacterial GEnome Annotation ComparisON), a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.

BlastKOLA: Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to this server and can be executed in an interactive mode. BlastKOALA is suitable for annotating fully sequenced genomes.

PAGIT: Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.

MAKER: A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).

MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

As with most programs that run on UNIX, the text output is in some specific format. If the program is popular enough, there will be one or more parsers written for that format – these are just utilities written to help you retrieve whatever information you are interested in from the output.

Let’s conclude this tutorial by converting the BLAST output in out.txt into a spreadsheet format, using a Python script. 

First, we need to get the script. We’ll do that using the ‘git’ program:

git clone https://github.com/ngs-docs/ngs-scripts.git /root/ngs-scripts

We’ll discuss ‘git’ more later; for now, just think of it as a way to get ahold of a particular set of files. In this case, we’ve placed the files in /root/ngs-scripts/, and you’re looking to run the script blast/blast-to-csv.py using Python:

python /root/ngs-scripts/blast/blast-to-csv.py out.txt

This outputs a spread-sheet like list of names and e-values. To save this to a file, do:

python /root/ngs-scripts/blast/blast-to-csv.py out.txt > ~out.csv

If you have Excel installed, try double clicking on it.

• the Damerau–Levenshtein distance allows insertion, deletion, substitution, and the transposition of two adjacent characters;
• the longest common subsequence (LCS) distance allows only insertion and deletion, not substitution;
• the Hamming distance allows only substitution, hence, it only applies to strings of the same length.
• the Jaro distance allows only transposition.

use Text::Levenshtein qw(distance);

 print distance("foo","four");
 # prints "2"

 my @words     = qw/ four foo bar /;
 my @distances = distance("foo",@words);

 print "@distances";
 # prints "2 0 3"

use Algorithm::LCSS qw( LCSS CSS CSS_Sorted );
    my $lcss_ary_ref = LCSS( \@SEQ1, \@SEQ2 );  # ref to array
    my $lcss_string  = LCSS( $STR1, $STR2 );    # string
    my $css_ary_ref = CSS( \@SEQ1, \@SEQ2 );    # ref to array of arrays
    my $css_str_ref = CSS( $STR1, $STR2 );      # ref to array of strings
    my $css_ary_ref = CSS_Sorted( \@SEQ1, \@SEQ2 );  # ref to array of arrays
    my $css_str_ref = CSS_Sorted( $STR1, $STR2 );    # ref to array of strings

There are many different modules on CPAN for calculating the edit distance between two strings. Here's just a selection.

Text::LevenshteinXS and Text::Levenshtein::XS are both versions of the Levenshtein algorithm that require a C compiler, but will be a lot faster than this module.

The Damerau-Levenshtein edit distance is like the Levenshtein distance, but in addition to insertion, deletion and substitution, it also considers the transposition of two adjacent characters to be a single edit. The module Text::Levenshtein::Damerau defaults to using a pure perl implementation, but if you've installed Text::Levenshtein::Damerau::XS then it will be a lot quicker.

Text::WagnerFischer is an implementation of the Wagner-Fischer edit distance, which is similar to the Levenshtein, but applies different weights to each edit type.

Text::Brew is an implementation of the Brew edit distance, which is another algorithm based on edit weights.

Text::Fuzzy provides a number of operations for partial or fuzzy matching of text based on edit distance. Text::Fuzzy::PP is a pure perl implementation of the same interface.

String::Similarity takes two strings and returns a value between 0 (meaning entirely different) and 1 (meaning identical). Apparently based on edit distance.

Text::Dice calculates Dice's coefficient for two strings. This formula was originally developed to measure the similarity of two different populations in ecological research.

A survey of best practices for RNA-seq data analysis

RNA-seq workflow: gene-level exploratory analysis and DE

RNAseq analysis notes from Tommy Tang

Analysis of RNA ‐ Seq Data

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

EBI RNA-Seq exercise

An open RNA-Seq data analysis pipeline tutorial with an example

RNA-Seq Analysis Workflow

Transcript-level expression analysis of RNA-seq experiments

Following are the useful links:

Single Cell RNAseq data analysis Tutorial

A step-by-step workflow for low-level analysis of single-cell RNA-seq data

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

SCell: single-cell RNA-seq analysis software

https://github.com/diazlab/SCell

Beta-Poisson model for single-cell RNA-seq data analyses

https://github.com/nghiavtr/BPSC

Sincera: A Computational Pipeline for Single Cell RNA-Seq Profiling Analysis

https://research.cchmc.org/pbge/sincera.html

SC3 – consensus clustering of single-cell RNA-Seq data

http://biorxiv.org/content/early/2016/09/02/036558

Citrus: A toolkit for single cell sequencing analysis

http://biorxiv.org/content/early/2016/09/14/045070

Single-Cell Resolution of Temporal Gene Expression during Heart Development

http://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30682-7

Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects

http://biorxiv.org/content/early/2016/11/15/087775

Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes

http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract

SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

http://biorxiv.org/content/early/2016/11/21/088856

SCOUP is a probabilistic model to analyze single-cell expression data during differentiation

https://github.com/hmatsu1226/SCOUP

scLVM is a modelling framework for single-cell RNA-seq data

https://github.com/PMBio/scLVM

Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories

https://github.com/jw156605/SLICER

SinQC: A Method and Tool to Control Single-cell RNA-seq Data Quality

http://www.morgridge.net/SinQC.html

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

https://github.com/zji90/TSCAN

Visualization and cellular hierarchy inference of single-cell data using SPADE

http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html

OEFinder: Identify ordering effect genes in single cell RNA-seq data

https://github.com/lengning/OEFinder

Again, running spades.py will show you the options:

spades.py

This produces:

SPAdes genome assembler v3.10.1

Usage: /usr/local/SPAdes-3.10.1-Linux/bin/spades.py [options] -o <output_dir>

Basic options:
-o      <output_dir>    directory to store all the resulting files (required)
--sc                    this flag is required for MDA (single-cell) data
--meta                  this flag is required for metagenomic sample data
--rna                   this flag is required for RNA-Seq data
--plasmid               runs plasmidSPAdes pipeline for plasmid detection
--iontorrent            this flag is required for IonTorrent data
--test                  runs SPAdes on toy dataset
-h/--help               prints this usage message
-v/--version            prints version

Input data:
--12    <filename>      file with interlaced forward and reverse paired-end reads
-1      <filename>      file with forward paired-end reads
-2      <filename>      file with reverse paired-end reads
-s      <filename>      file with unpaired reads
--pe<#>-12      <filename>      file with interlaced reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-1       <filename>      file with forward reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-2       <filename>      file with reverse reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-s       <filename>      file with unpaired reads for paired-end library number <#> (<#> = 1,2,..,9)
--pe<#>-<or>    orientation of reads for paired-end library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--s<#>          <filename>      file with unpaired reads for single reads library number <#> (<#> = 1,2,..,9)
--mp<#>-12      <filename>      file with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-1       <filename>      file with forward reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-2       <filename>      file with reverse reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-s       <filename>      file with unpaired reads for mate-pair library number <#> (<#> = 1,2,..,9)
--mp<#>-<or>    orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--hqmp<#>-12    <filename>      file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-1     <filename>      file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-2     <filename>      file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-s     <filename>      file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9)
--hqmp<#>-<or>  orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; <or> = fr, rf, ff)
--nxmate<#>-1   <filename>      file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--nxmate<#>-2   <filename>      file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,..,9)
--sanger        <filename>      file with Sanger reads
--pacbio        <filename>      file with PacBio reads
--nanopore      <filename>      file with Nanopore reads
--tslr  <filename>      file with TSLR-contigs
--trusted-contigs       <filename>      file with trusted contigs
--untrusted-contigs     <filename>      file with untrusted contigs

Pipeline options:
--only-error-correction runs only read error correction (without assembling)
--only-assembler        runs only assembling (without read error correction)
--careful               tries to reduce number of mismatches and short indels
--continue              continue run from the last available check-point
--restart-from  <cp>    restart run with updated options and from the specified check-point ('ec', 'as', 'k<int>', 'mc')
--disable-gzip-output   forces error correction not to compress the corrected reads
--disable-rr            disables repeat resolution stage of assembling

Advanced options:
--dataset       <filename>      file with dataset description in YAML format
-t/--threads    <int>           number of threads
                                [default: 16]
-m/--memory     <int>           RAM limit for SPAdes in Gb (terminates if exceeded)
                                [default: 250]
--tmp-dir       <dirname>       directory for temporary files
                                [default: <output_dir>/tmp]
-k              <int,int,...>   comma-separated list of k-mer sizes (must be odd and
                                less than 128) [default: 'auto']
--cov-cutoff    <float>         coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
--phred-offset  <33 or 64>      PHRED quality offset in the input reads (33 or 64)
                                [default: auto-detect]

As you can see this is also a “pipeline” of tools that can be switched on or off. SPAdes takes quite a long time, so for the purposes of this practical, something like this may suffice:

spades.py -t 4 \
          -m 32 \
          -k 31,51,71 \
          --only-assembler \
          -1 miseq.1.fastq -2 miseq.2.fastq \
          --nanopore minion.fastq \
          -o hybrid_assembly

In turn, these parameters mean

• use 4 threads
• max memory is 32Gb
• use 3 kmer values to build the de bruijn graph(s) - 31, 51 and 71
• only run the assembler, not the correction algorithm (for speed)
• read 1 and read 2 of the MiSeq data
• the nanopore data
• put the output in folder “hybrid_assembly”

kallisto

ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by reproduction.

apomorphy -- specialized (=derived) characters of an organism.

basal group -- The earliest diverging group within a clade; for instance, to hypothesize that sponges are basal animals is to suggest that the lineage(s) leading to sponges diverged from the lineage that gave rise to all other animals.

biological classification -- The orderly arrangement of organisms in hierarchical system that ideally reflects evolutionary history.

cDNA -- Complementary DNA; DNA that is synthesized, by reverse transcriptase, from a Messenger RNA template ( Messenger RNA contains the coded information for protein synthesis).

character -- Heritable trait possessed by an organism.

character state -- characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.

clade -- A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig.

cladogenesis -- The development of a new clade; the splitting of a single lineage into two distinct lineages; speciation.

cladogram -- A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.

convergence -- Similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology. 

crown group -- All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.

derived -- Describes a character state that is present in one or more subclades, but not all, of a clade under consideration. A derived character state is inferred to be a modified version of the primitive condition of that character, and to have arisen later in the evolution of the clade. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

diversity -- Term used to describe numbers of taxa, or variation in morphology. 

evolution -- Darwin's definition: descent with modification. The term has been variously used and abused since Darwin to include everything from the origin of man to the origin of life.

evolutionary tree -- A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.

expressed sequence tag (EST) -- A partial coding sequence isolated at random from a cDNA library, used for identification and mapping of coding sequences, for discovery of new genes and (by reference to sequence data banks) for discovery of identities with other genes.

extinction -- When all the members of a clade or taxon die, the group is said to be extinct.

genetic marker -- A DNA sequence that can be recognized and thus used to characterize the larger DNA sequence and the chromosome in which it occurs. 

homolog -- A feature that appears similar in two or more taxa with a common ancestor that also possessed that feature.

homology -- Two structures are considered homologous when they are inherited from a common ancestor which possessed the structure. This may be difficult to determine when the structure has been modified through descent.

hypothesis -- A concept or idea that can be falsified by various scientific methods.

ingroup -- In a cladistic analysis, the set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup.

lineage -- Any continuous line of descent; any series of organisms connected by reproduction by parent of offspring.

monophyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade.

outgroup -- In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other.

paraphyletic -- Term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor.

parsimony -- Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.

phylogenetics -- Field of biology that deals with the relationships between organisms. It includes the discovery of these relationships, and the study of the causes behind this pattern.

phylogeny -- The evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered.

plesiomorphy -- A primitive character state for the taxa under consideration.

polarity of characters -- The states of characters used in a cladistic analysis, either original or derived. Original characters are those acquired by an ancestor deeper in the phylogeny than the most recent common ancestor of the taxa under consideration. Derived characters are those acquired by the most recent common ancestor of the taxa under consideration.

polyphyletic -- Term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group.

primitive -- Describes a character state that is present in the common ancestor of a clade. A primitive character state is inferred to be the original condition of that character within the clade under consideration. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.

radiation -- Event of rapid cladogenesis, believed to occur under conditions where a new feature permits a lineage to move into a new niche or new habitat, and is then called an adaptive radiation.

rank -- In traditional taxonomy, taxa are ranked according to their level of inclusiveness. Thus a genus contains one or more species, a family includes one or more genera, and so on.

relatedness -- Two clades are more closely related when they share a more recent common ancestor between them than they do with any other clade.

repetitive DNA -- Sequences of DNA that are found to be repeated, sometimes thousands of times over.  

reticulation -- Joining of separate lineages on a phylogenetic tree, generally through hybridization or through lateral gene transfer. Fairly common in certain land plant clades; reticulation is thought to be rare among metazoans.

selection -- Process which favors one feature of organisms in a population over another feature found in the population. This occurs through differential reproduction -- those with the favored feature produce more offspring than those with the other feature, such that they become a greater percentage of the population in the next generation.

sister group -- The two clades resulting from the splitting of a single lineage.

stem group -- All the taxa in a clade preceding a major cladogenesis event. They are often difficult to recognize because they may not possess synapomorpies found in the crown group.

sympleisiomorphy – A ancestral character shared by the taxa under consideration

synapomorphy -- A character which is derived, and because it is shared by the taxa under consideration, is used to infer common ancestry (shared derived state).

synteny -- Portions of chromosomes in which gene order is conserved. 

systematics -- Field of biology that deals with the diversity of life. Systematics is usually divided into the two areas of phylogenetics and taxonomy.

taxon -- Any named group of organisms, not necessarily a clade

taxonomy -- The science of naming and classifying organisms. 

• 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