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

G T A T C G C T A Genome Analysis… Genome Analysis Toolkit-Queue

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…

G T A T C G C T A High-throUghput… High-throUghput GEnome SEQuencing

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…

G T A T C G C T A MANTEIA MANTEIA

MANTEIA

Allows the comparison of embryological, expression, molecular and etiological…

Allows the comparison of embryological, expression, molecular and etiological data from human, mouse, chicken and zebrafish simultaneously to identify new functional and structural correlations and…

G T A T C G C T A GenomeCloud GenomeCloud

GenomeCloud

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

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

Desktop app
G T A T C G C T A SHORE SHORE

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.

G T A T C G C T A Crossbow Crossbow

Crossbow

A scalable software pipeline for whole genome resequencing analysis.

A scalable software pipeline for whole genome resequencing analysis.

Desktop app
G T A T C G C T A Chipster Chipster

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…

G T A T C G C T A CloVR CloVR

CloVR

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

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

Desktop app
G T A T C G C T A Next Generation… Next Generation Sequencing Eclipse Plugin

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.

Desktop app
G T A T C G C T A ngs_backbone ngs_backbone

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…

G T A T C G C T A Biology Virtual… Biology Virtual Collaborative Labs

BioVLAB Biology Virtual Collaborative Labs

Cloud Computing and a graphical workflow composer that uses distributed…

Cloud Computing and a graphical workflow composer that uses distributed computing resources ``on demand.''

Desktop app
G T A T C G C T A ASAP ASAP

ASAP

An open source framework for building and executing a pipeline to preprocess…

An open source framework for building and executing a pipeline to preprocess next generation sequence data and variant calls.

Desktop app
G T A T C G C T A Reproductible… Reproductible Analyses for Bioinformatics

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…

Desktop app
G T A T C G C T A PYthon Comparative… PYthon Comparative GENomic Toolkit

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…

Desktop app
G T A T C G C T A Gene Identification… Gene Identification via Phenotype Sequencing

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…

Desktop app
G T A T C G C T A MutAid MutAid

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…

Desktop app
G T A T C G C T A Multi-Locus… Multi-Locus Geno-Typing

mlgt Multi-Locus Geno-Typing

Processing and analysis of high throughput (Roche 454) sequences generated from…

Processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and…

Desktop app
G T A T C G C T A RTG Variant RTG Variant

RTG Variant

The product line encompasses distinct products for the specific needs of…

The product line encompasses distinct products for the specific needs of clinical research, saving time and money while allowing customers to focus on the answers they need most.

Desktop app
G T A T C G C T A Pygr Pygr

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…

Web app
G T A T C G C T A transPLANT transPLANT

transPLANT

A plant informatics infrastructure. transPLANT is a virtualization platform,…

A plant informatics infrastructure. transPLANT is a virtualization platform, that provides access to specific genomic applications and workflows. transPLANT develops integrated standards and…

Desktop app
G T A T C G C T A NGS-QCbox NGS-QCbox

NGS-QCbox 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…

Desktop app
G T A T C G C T A Pipelines for… Pipelines for Evaluating Prokaryotic References

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…

Desktop app
G T A T C G C T A SeqMule SeqMule

SeqMule

A computational pipeline to perform automated variant calling from NGS data on…

A computational pipeline to perform automated variant calling from NGS data on human genomes and exomes. SeqMule integrates computational-cluster-free parallelization capability built on top of the…

Desktop app
G T A T C G C T A Software for Flexible… Software for Flexible Integration of Annotation

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…

Web app
G T A T C G C T A GeneWarrior GeneWarrior

GeneWarrior

An online sequence manipulation tool to perform common tasks such as managing…

An online sequence manipulation tool to perform common tasks such as managing sequences, calculating the reverse complement of a sequence, translating nucleotide to protein sequences, creating…

Desktop app
G T A T C G C T A EaSeq EaSeq

EaSeq

An agile computational environment which provides 1) extensive interactive…

An agile computational environment which provides 1) extensive interactive visualization, 2) combines the exploratory power of genome browsers with a comprehensive set of user-friendly tools for…

G T A T C G C T A Genomes on the Cloud Genomes on the Cloud

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,…

Desktop app
G T A T C G C T A TOolbox for Generic… TOolbox for Generic nGs anaLysEs

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…

Desktop app
G T A T C G C T A BALSA BALSA

BALSA

An integrated solution for the secondary analysis of next generation sequencing…

An integrated solution for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate…

Web app
G T A T C G C T A RepExplore RepExplore

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…

Desktop app
Web app
G T A T C G C T A QuickNGS QuickNGS

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…

G T A T C G C T A Churchill Churchill

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…

Desktop app
G T A T C G C T A gkno gkno

gkno

A set of tools and a framework to link tools together into analyses pipelines.

A set of tools and a framework to link tools together into analyses pipelines.

G T A T C G C T A Scalable Tools for… Scalable Tools for Open-Source Read Mapping

STORMSeq Scalable Tools for Open-Source Read Mapping

A graphical interface cloud computing solution that does not require a parallel…

A graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping,…

G T A T C G C T A Omics Pipe Omics Pipe

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,…

Desktop app
G T A T C G C T A SMRT-Analysis SMRT-Analysis

SMRT-Analysis

Open-source bioinformatics software suite for sequence alignment, assembly,…

Open-source bioinformatics software suite for sequence alignment, assembly, variant detection, and base modification discovery.

Desktop app
G T A T C G C T A Pipeliner Pipeliner

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…

G T A T C G C T A SpeedSeq SpeedSeq

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…

G T A T C G C T A Gaea Gaea

Gaea

Distribute re-sequencing computation to a cluster of nodes based on the Hadoop…

Distribute re-sequencing computation to a cluster of nodes based on the Hadoop Streaming framework with personalized algorithm interfaces for SOAP and BWA.

G T A T C G C T A Jnomics Jnomics

Jnomics

A collection of cloud-scale DNA sequence analysis tools.

A collection of cloud-scale DNA sequence analysis tools.

G T A T C G C T A Mercury Mercury

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.

G T A T C G C T A Bionimbus Bionimbus

Bionimbus

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

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

G T A T C G C T A GenomicTools GenomicTools

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…

Desktop app
G T A T C G C T A Lab7 Lab7

Lab7

A comprehensive workflow solution for providers, users and managers of…

A comprehensive workflow solution for providers, users and managers of next-generation sequencing services.

Web app
G T A T C G C T A HiPipe HiPipe

HiPipe

Provides high performance NGS data analysis pipelines with intuitive user…

Provides high performance NGS data analysis pipelines with intuitive user interface to the community so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS…

Desktop app
G T A T C G C T A ERGO ERGO

ERGO

Provides a systems biology informatics toolkit centered on comparative genomics…

Provides a systems biology informatics toolkit centered on comparative genomics to capture, query, and visualize sequenced genomes.  Using Igenbio's proprietary algorithms, and the most…

G T A T C G C T A Biodoop Biodoop

Biodoop

A suite of parallel bioinformatics applications based upon a popular…

A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop.

G T A T C G C T A Seven Bridges Genomics Seven Bridges Genomics

Seven Bridges Genomics

A cloud platform for next-generation sequencing analysis.

A cloud platform for next-generation sequencing analysis.

G T A T C G C T A Tute Genomics Tute Genomics

Tute Genomics

A robust, secure, medical-grade, web application that lives in the cloud and…

A robust, secure, medical-grade, web application that lives in the cloud and has the ability to analyze and annotate entire human genomes in a rapid and cost-effective way.

G T A T C G C T A BaseSpace BaseSpace

BaseSpace

The first cloud platform to be directly integrated in to the industry’s…

The first cloud platform to be directly integrated in to the industry’s leading sequencing platforms, with no cumbersome and time consuming data transfer steps.

Desktop app
G T A T C G C T A Genomatix Solutions Genomatix Solutions

Genomatix Solutions

With their unique combination of proprietary algorithms and comprehensive data…

With their unique combination of proprietary algorithms and comprehensive data background, all our solutions do more than enable you to efficiently and effectively analyze and interpret biological…

Desktop app
G T A T C G C T A Geospiza Geospiza

Geospiza

Develops software systems to accelerate genetic research.

Develops software systems to accelerate genetic research.

Desktop app
G T A T C G C T A JMP Genomics JMP Genomics

JMP Genomics

Provides the tools you need to analyze rare and common variants, detect…

Provides the tools you need to analyze rare and common variants, detect differential expression patterns, discover reliable biomarker profiles, and incorporate pathway information into your analysis…

Desktop app
G T A T C G C T A Lasergene Genomics… Lasergene Genomics Suite

Lasergene Genomics Suite

Next-Gen Sequence Assembly and Analysis.

Next-Gen Sequence Assembly and Analysis.

Desktop app
G T A T C G C T A NARWHAL NARWHAL

NARWHAL

Automates the primary analysis of massive parallel sequencing data.

Automates the primary analysis of massive parallel sequencing data.

Desktop app
G T A T C G C T A NextGENe NextGENe

NextGENe

Software for Next Generation (NGS) Sequence Analysis.

Software for Next Generation (NGS) Sequence Analysis.

Desktop app
G T A T C G C T A Partek Genomics Suite Partek Genomics Suite

Partek Genomics Suite

A comprehensive suite of advanced statistics and interactive data visualization…

A comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data.

Desktop app
G T A T C G C T A SeqGene SeqGene

SeqGene

An open-source software for mining next-gen sequencing datasets, focusing on…

An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc.

G T A T C G C T A bcbio-nextgen bcbio-nextgen

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

Desktop app
G T A T C G C T A BioDiscovery BioDiscovery

BioDiscovery

Advanced software solutions for individuals through enterprises…

Advanced software solutions for individuals through enterprises…

Desktop app
G T A T C G C T A CASAVA CASAVA

CASAVA

It can generate the following data: Sample-specific reads from multiplexed flow…

It can generate the following data: Sample-specific reads from multiplexed flow cells, aligned reads, SNP calls, indel calls and expression levels for exons, genes and splice junctions in the RNA…

Desktop app
G T A T C G C T A CLC Genomics Workbench CLC Genomics Workbench

CLC Genomics Workbench

A comprehensive and user-friendly analysis package for analyzing, comparing,…

A comprehensive and user-friendly analysis package for analyzing, comparing, and visualizing next generation sequencing data.

Desktop app
G T A T C G C T A Strand NGS Strand NGS

Strand NGS

An integrated platform that provides analysis, management and visualization…

An integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq,…

Desktop app
G T A T C G C T A Array Studio Array Studio

Array Studio

Provides the premier enterprise solution for data content, framework and…

Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…

Desktop app
Genedata Expressionist Genedata Expressionist

Genedata Expressionist

A comprehensive, enterprise software solution that manages, analyzes, and…

A comprehensive, enterprise software solution that manages, analyzes, and visualizes massive amounts of raw data from next-generation sequencing, microarray and other genomic technologies.

Desktop app
G T A T C G C T A LifeScope LifeScope

LifeScope

Leverages years of customer feedback and development for analysis tools for…

Leverages years of customer feedback and development for analysis tools for SOLiD system data, to enable faster translation of next-generation data to biologically meaningful results. Designed to…

Desktop app
G T A T C G C T A reseqtools reseqtools

reseqtools

A Toolkit for analyzing next-generation DNA Re-Sequencing data.

A Toolkit for analyzing next-generation DNA Re-Sequencing data.

Desktop app
G T A T C G C T A Bamformatics Bamformatics

Bamformatics

The project aims to provide a coherent and consistent approach to analysis of…

The project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data.

Desktop app
G T A T C G C T A draw-sneakpeek draw-sneakpeek

draw-sneakpeek

Analysis Workflow and Quality Metric Management for DNA-Seq Experiments.

Analysis Workflow and Quality Metric Management for DNA-Seq Experiments.

Desktop app
G T A T C G C T A GensearchNGS GensearchNGS

GensearchNGS

An integrated software solution for the analysis of DNA-Seq data from commonly…

An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent.

Desktop app
G T A T C G C T A Mutation Finder Mutation Finder

MutFinder Mutation Finder

It streamlines the next generation sequencing data analysis using BFAST for…

It streamlines the next generation sequencing data analysis using BFAST for aligner, SAMTOOLS for SNP caller, and ANNOVAR for annotation.

Desktop app
G T A T C G C T A NGSpeAnalysis NGSpeAnalysis

NGSpeAnalysis

A pipeline using open-source tools which can implement a set of pair ended…

A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants…

G T A T C G C T A efficient Cloud-based… efficient Cloud-based Epistasis cOmputing

eCEO efficient Cloud-based Epistasis cOmputing

An efficient Cloud-based Epistasis cOmputing model for large scale epistatic…

An efficient Cloud-based Epistasis cOmputing model for large scale epistatic interaction in GWAS.

Desktop app
G T A T C G C T A GenoMiner Deprecated GenoMiner

GenoMiner

A next generation sequencing data analysis computer for biologists with or…

A next generation sequencing data analysis computer for biologists with or without IT background.

Desktop app
G T A T C G C T A OmicsOffice for NGS OmicsOffice for NGS

OmicsOffice for NGS

An advanced and user-friendly software solution for secondary and tertiary…

An advanced and user-friendly software solution for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

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