Whole-genome sequencing data analysis bioinformatics software tools

WGS analysis steps

Preprocessing & quality control

Data analysis

Annotation & interpretation

File, data & workflows

WGS analysis workflow

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WGS analysis workflow schema
Since 2005, whole-genome sequencing platforms have become widely available, reducing the cost of DNA sequencing by four orders of magnitude relative to Sanger sequencing (DNA sequencing costs; Metzker, 2010; Mardis, 2011). NGS technologies are being…

Whole-genome sequencing data analysis bioinformatics software tools

Most Recent Tools

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Sentieon TNseq
Desktop

Sentieon TNseq

Provides the same advantages over MuTect/MuTect2 as Sentieon DNAseq provides…

Provides the same advantages over MuTect/MuTect2 as Sentieon DNAseq provides over BWA-GATK: it is over 10X faster in core-hours, has no run-to-run difference, does no down-sampling in high coverage…

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Sentieon DNAseq
Desktop

Sentieon DNAseq

Implements the same mathematics used in the Broad Institute’s BWA-GATK…

Implements the same mathematics used in the Broad Institute’s BWA-GATK HaplotypeCaller 3.x Best Practice Workflow pipeline. Sentieon DNAseq is a pipeline includes a computing efficiency enhancement…

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ARSDA
Desktop

ARSDA Analyzing RNA-Seq Data

Alleviates the problem associated with storage, transmission and analysis of…

Alleviates the problem associated with storage, transmission and analysis of high-throughput sequencing (HTS) data. ARSDA can take as input .SRA files or .fastq files of many gigabytes, build an…

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SV2
Desktop

SV2 support-vector structural-variant genotyper

Implements a machine-learning algorithm for genotyping deletions and tandem…

Implements a machine-learning algorithm for genotyping deletions and tandem duplications from paired-end whole genome sequencing (WGS) data. SV2 can rapidly integrate variant calls from multiple…

Most Popular Tools

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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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Bowtie
Desktop

Bowtie

An ultrafast, memory-efficient short read aligner. It aligns short DNA…

An ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a…

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SNPdryad
Web

SNPdryad

A computational method that can predict deleterious effect of amino acid…

A computational method that can predict deleterious effect of amino acid substitutions occurred in human proteins. SNPdryad outperforms other leading algorithms in accurately predicting deleterious…

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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

Curators for WGS analysis

  • Catherine Breton's avatar image
    Catherine Breton
    Institut des Sciences de…

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