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
GATK-Queue
Cloud

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
HugeSeq
Cloud

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
Data

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
Cloud

GenomeCloud

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

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

G T A T C G C T A
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.

G T A T C G C T A
Crossbow
Cloud

Crossbow

A scalable software pipeline for whole genome resequencing analysis.

A scalable software pipeline for whole genome resequencing analysis.

G T A T C G C T A
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…

G T A T C G C T A
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.

G T A T C G C T A
CloVR
Cloud

CloVR

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

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

G T A T C G C T A
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…

G T A T C G C T A
BioVLAB
Cloud

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.''

G T A T C G C T A
Data Retriever
Desktop

Data Retriever

Automates the tasks of finding, downloading, and cleaning up publicly available…

Automates the tasks of finding, downloading, and cleaning up publicly available data. Data retriever reduces the time for a user to get most large datasets up and running by hours, and in some cases…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
MutAid
Desktop
Virtual

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…

G T A T C G C T A
mlgt
Desktop

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…

G T A T C G C T A
ASAP
Desktop

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.

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

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.

G T A T C G C T A
Nanopolish
Desktop

Nanopolish

Provides a nanopore consensus algorithm using a signal-level hidden Markov…

Provides a nanopore consensus algorithm using a signal-level hidden Markov model (HMM). The main subprograms of Nanopolish are: (i) nanopolish extract which extracts reads in FASTA or FASTQ format…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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,…

G T A T C G C T A
Pyicos
Desktop

Pyicos

Analyses mapped reads from diverse High-throughput sequencing (HTS)…

Analyses mapped reads from diverse High-throughput sequencing (HTS) experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. Pyicos is a command line utility for the…

G T A T C G C T A
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…

G T A T C G C T A
transPLANT
Web

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…

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

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…

G T A T C G C T A
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…

G T A T C G C T A
SeqMule
Desktop

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…

G T A T C G C T A
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…

G T A T C G C T A
GeneWarrior
Web

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…

G T A T C G C T A
EaSeq
Desktop

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
GotCloud
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,…

G T A T C G C T A
TOGGLE
Desktop
Docker

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…

G T A T C G C T A
BALSA
Desktop

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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
Churchill
Cloud

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…

G T A T C G C T A
gkno
Desktop

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
STORMSeq
Cloud

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
Cloud

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,…

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

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.

G T A T C G C T A
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…

G T A T C G C T A
SpeedSeq
Cloud

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
Cloud

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
Cloud

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
Cloud

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
Cloud

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
Library

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…

G T A T C G C T A
Lab7
Desktop

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.

G T A T C G C T A
HiPipe
Web

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…

G T A T C G C T A
ERGO
Desktop

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
Cloud

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…
Cloud

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
Cloud

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
Cloud

BaseSpace

Offers a wide variety of NGS (next-generation sequencing) data analysis…

Offers a wide variety of NGS (next-generation sequencing) data analysis applications that are developed or optimized by Illumina, or from a growing ecosystem of third-party app providers. BAseSpace…

G T A T C G C T A
Genomatix…
Desktop

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…

G T A T C G C T A
Geospiza
Desktop

Geospiza

Develops software systems to accelerate genetic research.

Develops software systems to accelerate genetic research.

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

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…

G T A T C G C T A
Lasergene…
Desktop

Lasergene Genomics Suite

Next-Gen Sequence Assembly and Analysis.

Next-Gen Sequence Assembly and Analysis.

G T A T C G C T A
NARWHAL
Desktop

NARWHAL

Automates the primary analysis of massive parallel sequencing data.

Automates the primary analysis of massive parallel sequencing data.

G T A T C G C T A
NextGENe
Desktop

NextGENe

Software for Next Generation (NGS) Sequence Analysis.

Software for Next Generation (NGS) Sequence Analysis.

G T A T C G C T A
Partek…
Desktop

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.

G T A T C G C T A
SeqGene
Desktop

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
Cloud

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.…

G T A T C G C T A
BioDiscovery
Desktop

BioDiscovery

Advanced software solutions for individuals through enterprises…

Advanced software solutions for individuals through enterprises…

G T A T C G C T A
CASAVA
Desktop

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…

G T A T C G C T A
CLC Genomics…
Desktop

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.

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

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,…

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

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)…

Genedata…
Desktop

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.

G T A T C G C T A
LifeScope
Desktop

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…

G T A T C G C T A
reseqtools
Desktop

reseqtools

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

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

G T A T C G C T A
Bamformatics
Desktop

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.

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

draw-sneakpeek

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

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

G T A T C G C T A
GensearchNGS
Desktop

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.

G T A T C G C T A
MutFinder
Desktop

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.

G T A T C G C T A
NGSpeAnalysis
Desktop

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
eCEO
Cloud

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.

G T A T C G C T A
GenoMiner
Desktop

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.

G T A T C G C T A
OmicsOffice…
Desktop

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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