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Workflow/pipeline software tools | Whole-genome sequencing

These software pipelines provide out-of-the box solutions for DNA sequencing analysis by chaining a number of specific analysis tools together.

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GATK-Queue
Desktop

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data…

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HugeSeq
Desktop

HugeSeq High-throUghput GEnome SEQuencing

An automated pipeline for detecting genetic variants from high-throughput…

An automated pipeline for detecting genetic variants from high-throughput genome sequencing. HugeSeq is a fully integrated system for genome analysis from mapping reads to the identification and…

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GenomeCloud
Desktop

GenomeCloud

A cloud platform for next-generation sequencing analysis and storage.

A cloud platform for next-generation sequencing analysis and storage.

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CLC Genomics…
Desktop

CLC Genomics Workbench

Allows to analyze, compare, and visualize next generation sequencing (NGS)…

Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and…

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SpeedSeq
Desktop

SpeedSeq

An open-source genome analysis platform that accomplishes alignment, variant…

An open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics…

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O-Miner
Web

O-Miner

Allows automated analysis and annotation of complex -omics data. O-Miner is a…

Allows automated analysis and annotation of complex -omics data. O-Miner is a solution for the analysis and exploitation of data. The software is composed of two analytical domains, genomics and…

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SHORE
Desktop

SHORE

A mapping and analysis pipeline for short read data produced on the Illumina…

A mapping and analysis pipeline for short read data produced on the Illumina platform.

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NGSEP
Desktop

NGSEP Next Generation Sequencing Eclipse Plugin

The main functionality of NGSEP is the variants detector, which allows to make…

The main functionality of NGSEP is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.

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Crossbow
Desktop

Crossbow

Searches for single nucleotide polymorphisms (SNPs) with cloud computing.…

Searches for single nucleotide polymorphisms (SNPs) with cloud computing. Crossbow is a Hadoop-based software tool that combines the speed of the short read aligner Bowtie with the accuracy of the…

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Chipster
Desktop

Chipster

A user-friendly analysis software tool for high-throughput data. Chipster…

A user-friendly analysis software tool for high-throughput data. Chipster contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can…

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GIPS
Desktop

GIPS Gene Identification via Phenotype Sequencing

A pipeline for sequencing-based direct gene cloning. GIPS considers a range of…

A pipeline for sequencing-based direct gene cloning. GIPS considers a range of experimental and data analysis choices in a sequencing-based forward genetics study to design an optimal procedure for…

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SoFIA
Desktop

SoFIA Software for Flexible Integration of Annotation

A framework for workflow-driven data integration with a focus on genomic…

A framework for workflow-driven data integration with a focus on genomic annotation. SoFIA conceptualises workflow templates as comprehensive workflows that cover as many data integration operations…

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GMS
Desktop

GMS Genome Modeling System

Detects, summarizes, visualizes, and interprets the various types of somatic…

Detects, summarizes, visualizes, and interprets the various types of somatic and germline events encountered in variant analysis. GMS makes open, high-throughput genome analysis available to groups…

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MC-GenomeKey
Desktop

MC-GenomeKey Multi-Cloud GenomeKey

Provides a multicloud based solution to detect and annotate mutations.…

Provides a multicloud based solution to detect and annotate mutations. MC-GenomeKey executes the variant analysis workflow for detecting and annotating mutations using cloud resources from different…

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SPANDx
Desktop

SPANDx Synergised Pipeline for Analysis of NGS Data in Linux

Consolidates several well-validated, open-source packages into a single tool,…

Consolidates several well-validated, open-source packages into a single tool, mitigating the need to learn and manipulate individual next-generation sequencing (NGS) programs. SPANDx is an all-in-one…

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Mercury
Desktop

Mercury

An automated, flexible, and extensible analysis workflow that provides accurate…

An automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts.

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PEPR
Desktop

PEPR Pipelines for Evaluating Prokaryotic References

A reproducible and transparent bioinformatics tool for characterizing the…

A reproducible and transparent bioinformatics tool for characterizing the reference genome of prokaryotic genomic materials. PEPR evaluates the quality, purity, and homogeneity of the reference…

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MutAid
Desktop

MutAid

A pipeline to analyze and interpret raw sequencing data produced by Sanger or…

A pipeline to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. MutAid performs format conversion, base calling, quality trimming, filtering, read…

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Aozan
Desktop

Aozan

Automatically handles data transfer, demultiplexing conversion and quality…

Automatically handles data transfer, demultiplexing conversion and quality control once a HiSeq run has been finished. Aozan is an automated post sequencing data processing pipeline. It is a…

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GotCloud
Desktop

GotCloud Genomes on the Cloud

A pipeline for efficiently detecting and genotyping high-quality variants from…

A pipeline for efficiently detecting and genotyping high-quality variants from large-scale sequencing data. GotCloud automates sequence alignment, sample-level quality control, variant calling,…

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PyCogent
Desktop

PyCogent PYthon Comparative GENomic Toolkit

A framework to provide a collection of rigourously validated tools for the…

A framework to provide a collection of rigourously validated tools for the manipulation and analysis of genome biology data sets. PyCogent is a fully integrated and thoroughly tested framework for…

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Churchill
Desktop

Churchill

A highly scalable, ultra-fast and fully automated analysis pipeline for the…

A highly scalable, ultra-fast and fully automated analysis pipeline for the discovery of genetic variation. Through implementation of novel deterministic parallelization techniques, Churchill allows…

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CloVR
Desktop

CloVR

The Cloud Virtual Resource supports user-friendly automated microbial sequence…

The Cloud Virtual Resource supports user-friendly automated microbial sequence analysis applications.

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Friend
Desktop

Friend

Provides structure visualization, sequence alignment, simple phylogeny analysis…

Provides structure visualization, sequence alignment, simple phylogeny analysis and extended features to perform more complex analyses of sequence structure relationships. Friend is a bioinformatics…

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ngs_backbone
Desktop

ngs_backbone

A bioinformatic pipeline created to work on next generation sequence (NGS)…

A bioinformatic pipeline created to work on next generation sequence (NGS) analysis as well as with Sanger sequences. It is capable of cleaning reads, prepare a novo assembly, map reads against a…

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Rabix
Desktop

Rabix Reproductible Analyses for Bioinformatics

A package designed to support computational reproducibility/recomputability…

A package designed to support computational reproducibility/recomputability through the use of standard workflow descriptions. Rabix is a software model that supports metadata integration, provenance…

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GenomicTools
Desktop

GenomicTools

A flexible computational platform, comprising both a command-line set of tools…

A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq…

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CIPHER
Desktop

CIPHER

Automates the processing and analysis of several commonly used Next Generation…

Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease…

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MO-FBA-FVA
Desktop

MO-FBA-FVA MultiObjective-FBA-FVA

Provides two multi-objective extensions of constraint-based models (CBMs) for…

Provides two multi-objective extensions of constraint-based models (CBMs) for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis…

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NGS-QCbox
Desktop

NGS-QCbox

A parallel, automated and rapid quality control pipeline for analyzing the next…

A parallel, automated and rapid quality control pipeline for analyzing the next generation sequencing big data of Illumina platform. NGS-QCbox that scales up to process hundreds or thousands of…

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SNPTB
Desktop

SNPTB

Analyzes whole genome sequencing (WGS) data. SNPTB is a python package that…

Analyzes whole genome sequencing (WGS) data. SNPTB is a python package that facilitates bench biologist’s access to computational software for single nucleotide polymorphisms (SNPs) calling. The…

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Dugong
Desktop

Dugong

Allows automated installation of bioinformatics tools in computational…

Allows automated installation of bioinformatics tools in computational environments. Dugong is a comprehensive Docker-based virtual desktop that integrates more than 3500 bioinformatics softwares…

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NGS-pipe
Desktop

NGS-pipe

Allows to develop tailored workflows for the analysis of whole-exome (WES),…

Allows to develop tailored workflows for the analysis of whole-exome (WES), whole-genome (WGS), and transcriptome (RNA-seq) sequencing data. NGS-pipe is an automated framework for the design of…

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NGS-Bits
Desktop

NGS-Bits

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal…

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal experiments. NGS-Bits is separate into four steps: (1) gather information from raw reads, (2) map reads, (3) extract variant…

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Index_investiga…
Desktop

Index_investigator

Tests if index switching is occurring in a given dataset. Index_investigator is…

Tests if index switching is occurring in a given dataset. Index_investigator is a script that provides a way to visualize switch for sequenced genomic datasets. This method shows that in samples,…

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w2rap
Desktop

w2rap WGS Wheat Robust Assembly Pipeline

Generates high-quality, low-cost, robust assemblies from genomes with different…

Generates high-quality, low-cost, robust assemblies from genomes with different levels of complexity. W2rap encompasses a full data processing workflow from raw reads to scaffolds, and crucially…

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NGSeasy
Desktop

NGSeasy Easy Analysis of Next Generation Sequencing

Develops, distributes and runs pipelines encapsulated in Docker containers.…

Develops, distributes and runs pipelines encapsulated in Docker containers. NGSeasy allows user to deploy any pipeline version in any environment (e.g. operating systems, workstations, clusters,…

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Pygr
Desktop

Pygr

An open source software designed to make it easy to do powerful sequence and…

An open source software designed to make it easy to do powerful sequence and comparative genomics analyses, even with extremely large multi-genome data sets. Pygr is a bioinformatics graph tool…

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RepExplore
Web

RepExplore

A web-service for omics data analysis exploiting the information captured in…

A web-service for omics data analysis exploiting the information captured in the variance of technical replicates to provide more reliable and informative differential expression and abundance…

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Omics Pipe
Desktop

Omics Pipe

A computational framework that automates multi-omics data analysis pipelines on…

A computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq,…

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ANGSD
Desktop

ANGSD

Analyses next generation sequencing (NGS) data. ANGSD can handle a number of…

Analyses next generation sequencing (NGS) data. ANGSD can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into…

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TOGGLE
Desktop

TOGGLE TOolbox for Generic nGs anaLysEs

A suite of tools able to design pipelines that manage large sets of NGS…

A suite of tools able to design pipelines that manage large sets of NGS softwares and utilities. Moreover, TOGGLE offers an easy way to manipulate the various options of the different softwares…

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Pipeliner
Desktop

Pipeliner

A tool to evaluate, by simulation, the performance of NGS pipelines in…

A tool to evaluate, by simulation, the performance of NGS pipelines in resequencing studies. Pipeliner provides a graphical interface allowing the users to write and test their own bioinformatics…

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QuickNGS
Desktop
Web

QuickNGS

A workflow system for laboratories with the need to analyze data from multiple…

A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and…

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Bionimbus
Desktop

Bionimbus

A cloud-based infrastructure for managing, analyzing and sharing genomics…

A cloud-based infrastructure for managing, analyzing and sharing genomics datasets.

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Toil
Desktop

Toil

Offers a way to manage pipelines. Toil supports arbitrary worker and leader…

Offers a way to manage pipelines. Toil supports arbitrary worker and leader failure, with strong check-pointing that allows resumption. It can be employed to run scientific workflows on a large scale…

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PipEngine
Desktop

PipEngine

Constructs shell scripts which can then be submitted automatically to a…

Constructs shell scripts which can then be submitted automatically to a scheduling system or run locally. PipEngine is particularly useful for next generation sequencing (NGS) but can work on any job…

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NextFlow
Desktop

NextFlow

Enables pipeline development through the adaptation of existing pipelines…

Enables pipeline development through the adaptation of existing pipelines written in any scripting language. NextFlow is a workflow management system using Docker technology for the multi-scale…

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C3S-LAA
Desktop

C3S-LAA Clustering of Circular Consensus Sequences for Long Amplicon Analysis of PacBio Data

Offers a platform for single molecule real-time (SMRT) sequencing error…

Offers a platform for single molecule real-time (SMRT) sequencing error correction and assembly for libraries of pooled amplicons. C3S-LAA is a pipeline dedicated to processing tiled amplicon…

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Sequana
Desktop

Sequana

Provides a set of flexible genomic pipelines for processing and reporting Next…

Provides a set of flexible genomic pipelines for processing and reporting Next Generation Sequencing (NGS) analysis. Sequana contains also some standalone applications: 1) sequana_coverage eases the…

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