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Workflow management systems | High-throughput sequencing

Bioinformatics pipelines can be modeled as workflows where each work item is a stage (executable) in the pipeline. Workflow management software allows for the creation and execution of workflows. They are available as both command line controlled…
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Snakemake
Desktop

Snakemake

Provides an execution environment with a clean and readable specification…

Provides an execution environment with a clean and readable specification language to reduce the complexity of creating workflows. Snakemake is a workflow engine inspired by the build system GNU…

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GenePattern
Desktop
Web

GenePattern

A powerful genomic analysis platform that provides access to more than 240…

A powerful genomic analysis platform that provides access to more than 240 tools for gene expression analysis, proteomics, SNP analysis, RNA-seq analysis, and common data tasks.

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Bio-Linux
Desktop

Bio-Linux

A powerful, free bioinformatics workstation platform that can be installed on…

A powerful, free bioinformatics workstation platform that can be installed on anything from a laptop to a large server, or run as a virtual machine. Bio-Linux 8 adds more than 250 bioinformatics…

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Galaxy
Web

Galaxy

An open-source, web platform that incorporates workflow technology and in-built…

An open-source, web platform that incorporates workflow technology and in-built access to bioinformatics resources including remote data warehouses and tools. Several public instances of Galaxy are…

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Genboree…
Desktop

Genboree Workbench

Manages the many technical software and hardware aspects of genome-centric…

Manages the many technical software and hardware aspects of genome-centric research for end-users. The Workbench contains bioinformatics tools useful for analyses in genomics, epigenomics,…

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Taverna
Desktop

Taverna

An open source and domain-independent Workflow Management System - a suite of…

An open source and domain-independent Workflow Management System - a suite of tools used to design and execute scientific workflows and aid in silico experimentation.

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Knime4Bio
Desktop

Knime4Bio

A set of custom nodes for the KNIME (The Konstanz Information Miner)…

A set of custom nodes for the KNIME (The Konstanz Information Miner) interactive graphical workbench, for the interpretation of large biological datasets. KNIME provides the ability to modify the…

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Anduril
Desktop

Anduril

A data integration framework for translating fragmented large-scale data into…

A data integration framework for translating fragmented large-scale data into testable predictions. The Anduril framework allows rapid integration of heterogeneous data with state-of-the-art…

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Ergatis
Desktop

Ergatis

A web interface and scalable software system for bioinformatics workflows.

A web interface and scalable software system for bioinformatics workflows.

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Singularity
Desktop

Singularity

Creates portable environments for scientific application. Singularity aims to…

Creates portable environments for scientific application. Singularity aims to support existing and traditional high-performance computing (HPC) resources by supplying portable and reproductible…

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wft4galaxy
Desktop

wft4galaxy WorkFlow Testing 4 Galaxy

Simplifies and automates workflow tests. wft4galaxy is a package to bring…

Simplifies and automates workflow tests. wft4galaxy is a package to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring…

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BioQueue
Desktop

BioQueue

Improves the efficiency and robustness of bioinformatics research. BioQueue…

Improves the efficiency and robustness of bioinformatics research. BioQueue provides a web-based workbench and implements an explicit syntax to keep an optimal balance between flexibility and…

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BETSY
Desktop

BETSY Bioinformatics ExperT SYstem

Allows to develop workflows in order to perform analyses. BETSY combines a rich…

Allows to develop workflows in order to perform analyses. BETSY combines a rich data model with an inference engine tuned to reduce the exponential expansion of the search. Users can specify a…

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Knime4NGS
Desktop

Knime4NGS

Consists of an extension of the open source platform KNIME by adding the…

Consists of an extension of the open source platform KNIME by adding the functionality for essential Next Generation Sequencing (NGS) data processing. KNIME4NGS is a comprehensive linux-based toolkit…

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BDS
Desktop

BDS BigDataScript

Simplifies implementing, testing and debugging complex data analysis pipelines.…

Simplifies implementing, testing and debugging complex data analysis pipelines. BDS is a scripting language designed for working with big data pipelines in system architectures of different sizes and…

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SparkSeq
Desktop

SparkSeq

Serves for RNA and DNA sequencing analyses. SparkSeq combines Picard Java…

Serves for RNA and DNA sequencing analyses. SparkSeq combines Picard Java Development Kit for Sequence Alignment/Map format (SAM) and Apache Spark to introduce versatile sequencing analyses in…

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Galaxy Portal…
Mobile

Galaxy Portal app

An open source interface to the Galaxy system through smartphones and tablets.…

An open source interface to the Galaxy system through smartphones and tablets. The Galaxy Portal app provides convenient and efficient monitoring of job completion, as well as opportunities for…

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qsubsec
Desktop

qsubsec

A template language for generating qsub files for submission using the Sun Grid…

A template language for generating qsub files for submission using the Sun Grid Engine system. By using this system, you can separate the logic of your qsub jobs from the specific data of a specific…

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Jflow
Desktop

Jflow

A JavaScript based workflow management system, composed of Jquery plugins which…

A JavaScript based workflow management system, composed of Jquery plugins which can easily be embedded in any WEB application and a Python library providing all requested features to setup, run and…

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OTP
Web

OTP One Touch Pipeline

Provides a platform for storing, handling and processing next generation…

Provides a platform for storing, handling and processing next generation sequencing (NGS) data. OTP performs both data management and processing and allows users to automate an entire process to raw…

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repo
Desktop

repo

Manages bioinformatic analysis. repo supports a data-centered philosophy that…

Manages bioinformatic analysis. repo supports a data-centered philosophy that aims at improving analysis reproducibility and reusability with minimal design overhead. It constitutes an unobtrusive…

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BioMAJ
Desktop

BioMAJ BIOlogie Mise A Jour

Maintains any set of data up to date. BioMAJ is a databank management software…

Maintains any set of data up to date. BioMAJ is a databank management software that handles all different steps of dataset management (updates monitoring, download, checking, processing, and more).…

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ZBIT…
Web

ZBIT Bioinformatics Toolbox

Provides web-based access to a collection of bioinformatics tools developed for…

Provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. ZBIT Bioinformatics Toolbox is designed to…

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Wobidisco
Desktop

Wobidisco

Gathers several tools bioinformatics. Wobidisco is composed of a set of…

Gathers several tools bioinformatics. Wobidisco is composed of a set of workflow-management-related projects. It contains: a general-purpose work ow engine (Ketrew); a library collecting and wrapping…

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Arteria
Desktop

Arteria

Allows users to realize modelling, and micro-services for action execution.…

Allows users to realize modelling, and micro-services for action execution. Arteria permits researchers to manage the full breadth of the operational aspects surrounding sequencing center operations.…

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Biopipe
Web
Desktop

Biopipe

Facilitates design and implementation of bioinformatics workflows and…

Facilitates design and implementation of bioinformatics workflows and applications, and allows comparison between alternative methods. Biopipe is a Docker-based system to assist the researchers in…

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BioContainers
Desktop

BioContainers

Allows labs of all sizes to easily install bioinformatics software, maintain…

Allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on…

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flowr
Desktop

flowr

A robust and scalable framework for designing and deploying computing pipelines…

A robust and scalable framework for designing and deploying computing pipelines in an easy scatter-gather approach. flowr provides input commands as a tab-delimited file, and a second tsv defining…

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Workflow…
Desktop

Workflow Conversion

A set of tools that enables the scientific community to benefit from workflow…

A set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line…

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NEAT
Desktop

NEAT NExt generation Analysis Toolbox

Assists users in management of ChIPseq and RNAseq pipelines. NEAT offers…

Assists users in management of ChIPseq and RNAseq pipelines. NEAT offers several automated modules: unzip, rename, QC, chiprx, map, filter, peakcalling, creation of wig files, etc. The latter can be…

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GVL
Web

GVL Genomics Virtual Laboratory

A pipeline implemented as a middleware layer of machine images, cloud…

A pipeline implemented as a middleware layer of machine images, cloud management tools, and online services. Genomics Virtual Laboratory enables researchers to build arbitrarily sized compute…

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BioVeL
Web

BioVeL

Provides a virtual portal for researchers that allows to run multiple…

Provides a virtual portal for researchers that allows to run multiple workflows. BioVel aims to supply a laboratory that gathers functionalities for supporting complex data biodiversity science and…

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Cluster Flow
Desktop

Cluster Flow

Allows users to manage bioinformatics tools. Cluster Flow is a workflow manager…

Allows users to manage bioinformatics tools. Cluster Flow is a workflow manager including 40 modules for common next-generation sequencing (NGS) processing steps. This tool can also be used on single…

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Glbase
Desktop

Glbase

Allows the user to perform many common analyses on ChIP-seq, microarray and…

Allows the user to perform many common analyses on ChIP-seq, microarray and RNA-seq data. Glbase is a flexible and multifunctional toolkit which includes many functions to intersect two lists of…

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Pegasus
Desktop

Pegasus

Maps abstract workflow descriptions onto distributed computing infrastructures.…

Maps abstract workflow descriptions onto distributed computing infrastructures. Pegasus has been used for more than twelve years by scientists in a wide variety of domains, including astronomy,…

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NextflowWorkben…
Desktop

NextflowWorkbench

A workflow system that was designed for both beginners and experts, and blends…

A workflow system that was designed for both beginners and experts, and blends the distinction between user interface and scripting language. This system extends and reuses the popular Nextflow…

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Kronos
Desktop

Kronos

A software platform for automating the development and execution of…

A software platform for automating the development and execution of reproducible, auditable and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by…

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COSMOS
Desktop

COSMOS

Manages large-scale workflows that allows formal description of pipelines and…

Manages large-scale workflows that allows formal description of pipelines and partitioning of jobs. COSMOS includes a user-interface for tracking the progress of jobs, abstraction of the job queuing…

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HTSstation
Desktop
Web

HTSstation

A suite of simple web forms coupled to modular analysis pipelines for various…

A suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing.

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DNAstack
Desktop

DNAstack

Permits to store genomics, bioinformatics data. DNAstack offers a way to share…

Permits to store genomics, bioinformatics data. DNAstack offers a way to share data on the cloud. It permits users to upload large or small datasets through a simple and fast drag and drop uploader.…

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Wings
Desktop

Wings Workflow INstance Generation and Specialization

Designs and explores computational experiments as workflows. Wings generates…

Designs and explores computational experiments as workflows. Wings generates vary as the system explores different choices of data sets and parameters. It permits to discover new combination of…

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PyCOMPSs
Desktop

PyCOMPSs

Facilitates the development of parallel computational workflows in Python. In…

Facilitates the development of parallel computational workflows in Python. In this approach, the user programs her script in a sequential fashion and decorates the functions to be run as asynchronous…

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pyvalid
Desktop

pyvalid

A flexible, lightweight and modest solution to the problem of annotating…

A flexible, lightweight and modest solution to the problem of annotating computational analyses in large research projects. This approach is independent of a specific software environment, results in…

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Galaxy@Pasteur
Web

Galaxy@Pasteur

A system to provide a flexible and usable Web environment for defining and…

A system to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce…

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Bioflow
Desktop

Bioflow

Designed to simplify the entire process of creating and executing workflows.

Designed to simplify the entire process of creating and executing workflows.

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DE
Desktop

DE DISCOVERY ENVIRONMENT

Provides a platform for handling data from various experiments. DE is a…

Provides a platform for handling data from various experiments. DE is a software, part of the Cyverse environment, developed for creating a simplified and customized graphic interface. The program…

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Roddy
Desktop

Roddy

Authorizes to develop and handle script based workflows. Roddy is a standalone…

Authorizes to develop and handle script based workflows. Roddy is a standalone software that aims to assist in managing community projects. It allows to include a wide range of workflows and gives…

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EvE
Web

EvE EvErything

Allows users to build a pipeline easily. EvE permits to align, call, annotate,…

Allows users to build a pipeline easily. EvE permits to align, call, annotate, convert and interpret any genetic data. It offers the possibility for users to select their approach for creating a…

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WAVES
Web

WAVES Web Application for Versatile & Easy bioinformatics Services

Provides a platform which can run any tool (nearly), assuming its executable…

Provides a platform which can run any tool (nearly), assuming its executable file with inputs and outputs. WAVES can launch jobs anywhere (virtually), locally, on cluster (over ssh or not), on any…

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Ketrew
Desktop

Ketrew

Provides an EDSL API to define complex and convoluted workflows…

Provides an EDSL API to define complex and convoluted workflows ((interdependent steps/programs using a lot of data, with many parameter variations, running on different hosts with various…

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CB-Commander
Desktop

CB-Commander

Assists biologists and computational biology researchers during the design and…

Assists biologists and computational biology researchers during the design and execution processes of their experiments. CB-Commander enables users to integrate different components of an experiment,…

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The R Project…
Desktop

The R Project for Statistical Computing

Allows statistical computing and graphics. The R Project for Statistical…

Allows statistical computing and graphics. The R Project for Statistical Computing is a software environment enabling data manipulation, data calculation and graphical display.

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BioExtract
Web

BioExtract

Harnesses the power of online informatics tools for creating and customizing…

Harnesses the power of online informatics tools for creating and customizing workflows.

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bioKepler
Desktop

bioKepler

A project that builds scientific workflow components to execute a set of…

A project that builds scientific workflow components to execute a set of bioinformatics tools using distributed execution patterns.

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HIVE
Desktop

HIVE High-performance Integrated Virtual Environment

A distributed storage and compute environment designed primarily to handle…

A distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized…

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Genephony
Web

Genephony

Serves as a browser for genomic data, as a high-throughput annotation tool, and…

Serves as a browser for genomic data, as a high-throughput annotation tool, and as a knowledge discovery tool. Genephony can manage large datasets of genomic information, integrating them with…

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