BOL: Related items

Alignment-free sequence comparison tools available for next-generation sequencing data analysis

Abhimanyu Singh — Tue, 07 Nov 2017 05:33:33 -0600

kallisto

Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)

Software (C++)

https://pachterlab.github.io/kallisto/

Sailfish

Estimation of isoform abundances from reference sequences and RNA-seq data (k-mer based)

Software (C++)

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Salmon

Quantification of the expression of transcripts using RNA-seq data (uses k-mers)

https://combine-lab.github.io/salmon/

RNA-Skim

RNA-seq quantification at transcript-level (partitions the transcriptome into disjoint transcript clusters; uses sig-mers, a special type of k-mers)

Software (C++)

http://www.csbio.unc.edu/rs/

Variant calling

ChimeRScope

Fusion transcript prediction using gene k-mers profiles of the RNA-seq paired-end reads

Software (Java)

https://github.com/ChimeRScope/ChimeRScope/wiki

FastGT

Genotyping of known SNV/SNP variants directly from raw NGS sequence reads by counting unique k-mers

Software (C)

https://github.com/bioinfo-ut/GenomeTester4/

Phy-Mer

Reference-independent mitochondrial haplogroup classifier from NGS data (k-mer based)

Software (Python)

https://github.com/danielnavarrogomez/phy-mer

LAVA

Genotyping of known SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from raw NGS reads (k-mer based)

Software (C)

http://lava.csail.mit.edu/

MICADo

Detection of mutations in targeted third-generation NGS data (can distinguish patients’ specific mutations; algorithm uses k-mers and is based on colored de Bruijn graphs)

Software (Python)

http://github.com/cbib/MICADo

General mapper

Minimap

Lightweight and fast read mapper and read overlap detector (uses the concept of “minimazers”, a special type of k-mers)

Software (C)

https://github.com/lh3/minimap

Assembly

De novo genome assembly

MHAP

Produces highly continuous assembly (fully resolved chromosome arms) from third-generation long and noisy reads (10 kbp) using a dimensionality reduction technique MinHash

Software (Java)

https://github.com/marbl/MHAP

Miniasm

Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Consensus (OLC) approach without the necessity of an error correction stage (uses minimap)

Software (C)

https://github.com/lh3/miniasm

LINKS

Scaffolding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes)

Software (Perl)

https://github.com/warrenlr/LINKS/

Read clustering

afcluster

Clustering of reads from different genes and different species based on k-mer counts

Software (C++)

https://github.com/luscinius/afcluster

QCluster

Clustering of reads with alignment-free measures (k-mer based) and quality values

Software (C++)

http://www.dei.unipd.it/~ciompin/main/qcluster.html

Reads error correction

Lighter

Correction of sequencing errors in raw, whole genome sequencing reads (k-mer based)

Software (C++)

https://github.com/mourisl/Lighter

QuorUM

Error corrector for Illumina reads using k-mers

Software (C++)

https://github.com/gmarcais/Quorum

Trowel

Software (C++)

https://sourceforge.net/projects/trowel-ec/

Metagenomics

Assembly-free phylogenomics

AAF

Phylogeny reconstruction directly from unassembled raw sequence data from whole genome sequencing projects; provides bootstrap support to assess uncertainty in the tree topology (k-mer based)

Software (Python)

https://github.com/fanhuan/AAF

kSNP v3

Reference-free SNP identification and estimation of phylogenetic trees using SNPs (based on k-mer analysis)

Software (C)

https://sourceforge.net/projects/ksnp/files/

NGS-MC

Phylogeny of species based on NGS reads using alignment-free sequence dissimilarity measures d2* and d2 S under different Markov chain models (using k-words)

R package

http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html

Species identification/taxonomic profiling

CLARK

Taxonomic classification of metagenomic reads to known bacterial genomes using k-mer search and LCA assignment

Software (C++)

http://clark.cs.ucr.edu/

FOCUS

Reports organisms present in metagenomic samples and profiles their abundances (uses composition-based approach and non-negative least squares for prediction)

Web service Software (Python)

http://edwards.sdsu.edu/FOCUS/

GSM

Estimation of abundances of microbial genomes in metagenomic samples (k-mer based)

Software (Go)

https://github.com/pdtrang/GSM

Mash

Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimensionality-reduction technique)

Software (C++)

https://github.com/marbl/mash

Kraken

Taxonomic assignment in metagenome analysis by exact k-mer search; LCA assignment of short reads based on a comprehensive sequence database

Software (C++)

https://ccb.jhu.edu/software/kraken/

LMAT

Assignment of taxonomic labels to reads by k-mers searches in precomputed database

Software (C++/Python)

https://sourceforge.net/projects/lmat/

stringMLST

k-mer-based tool for MLST directly from the genome sequencing reads

Software (Python)

http://jordan.biology.gatech.edu/page/software/stringMLST

Taxonomer

k-mer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from clinical and environmental samples

Web service

http://taxonomer.iobio.io/

Other

d2-tools

Word-based (k-tuple) comparison (pairwise dissimilarity matrix using d2S measure) of metatranscriptomic samples from NGS reads

Software (Python/R)

https://code.google.com/p/d2-tools/

VirHostMatcher

Prediction of hosts from metagenomic viral sequences based on ONF using various distance measures (e.g., d2)

Software (C++)

https://github.com/jessieren/VirHostMatcher

MetaFast

Statistics calculation of metagenome sequences and the distances between them based on assembly using de Bruijn graphs and Bray–Curtis dissimilarity measure

Software (Java)

https://github.com/ctlab/metafast

Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Jit — Tue, 26 Dec 2017 22:23:39 -0600

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data

Jit — Mon, 06 Aug 2018 17:24:53 -0500

NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV is in ANNOVAR-compatible bed format. Users can easily perform downstream annotation using ANNOVAR and disease gene discovery using Phenolyzer.

Address of the bookmark: https://github.com/Nextomics/NextSV

Qualimap2: Evaluating next generation sequencing alignment data

Jit — Tue, 11 Sep 2018 04:44:29 -0500

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Supported types of experiments include:

Whole-genome sequencing
Whole-exome sequencing
RNA-seq (speical mode available)
ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

AMStat: display statistics of large sequence files from next generation sequencing projects

Neel — Fri, 09 Nov 2018 13:34:56 -0600

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

Address of the bookmark: http://samstat.sourceforge.net/

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Radha Agarkar — Fri, 04 Jan 2019 10:10:48 -0600

EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/.

EXCAVATOR is a novel software package for the detection of copy number variants (CNVs) from whole-exome sequencing data.
EXCAVATOR has been published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abstract).

Address of the bookmark: https://sourceforge.net/projects/excavatortool/

Prof. Dr. med. Andreas Ramming

Wed, 07 Aug 2019 03:25:48 -0500

In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of patients respond to these existing therapies on a permanent basis. In the remaining cases, these therapies miss their target from the beginning or later during the course of treatment failure. There are currently no causal therapies available for the treatment of fibrotic autoimmune diseases such as systemic sclerosis. Therefore, there is an urgent need to develop new therapeutic options for the treatment of fibrotic and synovitic autoimmune diseases. His group is therefore deal with the molecular mechanisms of these misdirected signaling pathways for the development of novel, targeted therapies

http://www.medizin3.uk-erlangen.de/forschung/arbeitsgruppen/matrixbiologie-entzuendliche-signalwege-in-arthritis-und-fibrose/

DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Jit — Sat, 25 Jan 2020 13:28:09 -0600

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on Nucleus, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the TensorFlow machine learning framework.

https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html

https://www.biorxiv.org/content/10.1101/092890v6

Address of the bookmark: https://github.com/google/deepvariant

McClintock: Meta-pipeline to identify transposable element insertions using next generation sequencing data

BioStar — Tue, 27 Oct 2020 00:21:18 -0500

an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae.

Address of the bookmark: https://github.com/bergmanlab/mcclintock

Pollux: platform independent error correction of single and mixed genomes

Jit — Fri, 19 May 2017 09:41:27 -0500

Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0435-6

Address of the bookmark: https://github.com/emarinier/pollux