High throughput sequencing (HTS) has become one of the primary experimental tools used to extract genomic information from biological samples. Bioinformatics tools are continuously being developed for the analysis of HTS data. Beyond some well-defined core analyses, such as…
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Snakemake
Desktop

Snakemake

A Python based language and execution environment for make-like workflows.

A Python based language and execution environment for make-like workflows.

CLOUD
BioPig
Cloud

BioPig

A framework for genomic data analysis using Apache Pig and Hadoop.

A framework for genomic data analysis using Apache Pig and Hadoop.

CLOUD
Eoulsan
Cloud

Eoulsan

A versatile framework based on the Hadoop implementation of the MapReduce…

A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.

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MolBioLib
Desktop

MolBioLib

A compact, portable, and extensively tested C++11 software framework and set of…

A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications.

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Yabi
Cloud

Yabi

A software system that is adaptable to a range of both pluggable execution and…

A software system that is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC…

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GenomeTools
Desktop

GenomeTools

Follows the annotation graph approach, offering a unified graph-based…

Follows the annotation graph approach, offering a unified graph-based representation. GenomeTools is a software library and an associated software tools for developing bioinformatics software…

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Hail
Desktop

Hail

Explores and analyzes genetic data. Hail can generate variant annotations like…

Explores and analyzes genetic data. Hail can generate variant annotations like call rate, Hardy-Weinberg equilibrium p-value, and population-specific allele count, generate sample annotations like…

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VisRseq
Desktop

VisRseq

Provides a visual framework for analysis of sequencing datasets. VisRseq is a…

Provides a visual framework for analysis of sequencing datasets. VisRseq is a computationally rich and accessible framework for integrative and interactive analyses without requiring programming…

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SeqAn
Desktop

SeqAn

Comprises implementations of existing, practical state-of-the-art algorithmic…

Comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. SeqAn is a library of efficient data types and…

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htslib
Desktop

htslib

Reads and writes high-throughput sequencing data. The htsfile utility attempts…

Reads and writes high-throughput sequencing data. The htsfile utility attempts to identify what kind of high-throughput sequencing data files the specified files are, and provides minimal viewing…

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Bioconductor
Desktop

Bioconductor

An open-source, open-development software project for the analysis and…

An open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research,…

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EBiAn
Desktop

EBiAn Easy Bioinformatics Analysis

Performs the main analysis and manipulation of DNA, RNA, proteins and peptides…

Performs the main analysis and manipulation of DNA, RNA, proteins and peptides sequences. EBiAn offers tools to enable the more routinely analysis used in preliminary computational approaches to…

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pandas
Desktop

pandas

Aims to be the fundamental high-level building block for doing practical, real…

Aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. pandas is a Python package providing fast, flexible, and expressive data structures…

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bíogo
Desktop

bíogo

Aims to ease development and maintenance of computationally intensive…

Aims to ease development and maintenance of computationally intensive bioinformatics applications. The bíogo library is written in the Go programming language, a garbage-collected, strictly typed…

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Bioclojure
Library

Bioclojure

A functional software library written in the language Clojure specifically…

A functional software library written in the language Clojure specifically designed for parsing and processing biological sequence data. Bioclojure provides a lazy and thread-safe framework for…

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SUSHI
Desktop

SUSHI Support Users for SHell-script Integration

An agile data analysis framework that relieves bioinformaticians from the…

An agile data analysis framework that relieves bioinformaticians from the administrative challenges of their data analysis. SUSHI lets users build reproducible data analysis workflows from individual…

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i2x
Desktop

i2x

A reactive and event-driven framework that simplifies real-time data…

A reactive and event-driven framework that simplifies real-time data integration and interoperability. This platform facilitates otherwise difficult tasks, such as connecting heterogeneous services,…

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GenOO
Desktop

GenOO

An open-source, object-oriented (OO) Perl framework specifically developed for…

An open-source, object-oriented (OO) Perl framework specifically developed for the design and implementation of HTS analysis tools. GenOO models biological entities such as genes and transcripts as…

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Rust-Bio
Library

Rust-Bio

A general purpose bioinformatics library for the innovative Rust programming…

A general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to…

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CracTools
Desktop

CracTools

Integrated pipelines for RNA-Seq analysis using CRAC (mapping tool) additional…

Integrated pipelines for RNA-Seq analysis using CRAC (mapping tool) additional fields. CracTools are a complete toolbox designed to build pipelines on top of CRAC. CracTools are based on the…

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BioJS
Desktop

BioJS

An open-source project whose main objective is the visualization of biological…

An open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It…

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Rbbt
Desktop

Rbbt Ruby Bioinformatics Toolkit

A framework for software development in bioinformatics. Rbbt covers three…

A framework for software development in bioinformatics. Rbbt covers three aspects: 1) Developing functionalities, 2) making them as widely accessible as possible and 3) integrating them with one…

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Whiteboard
Desktop

Whiteboard

A class library implemented in C++ that enables visualization to be tightly…

A class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets. Whiteboard provides all basic tool sets for drawing…

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Ruffus
Desktop

Ruffus

A library for the creation of computational pipelines. Ruffus lightweight and…

A library for the creation of computational pipelines. Ruffus lightweight and unobtrusive design recommends it for use even for the most trivial of analyses. At the same time, it is powerful enough…

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BioRuby
Desktop

BioRuby

Contains a comprehensive set of free development tools and libraries for…

Contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis,…

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Mobyle SNAP…
Web

Mobyle SNAP Workbench

The web portal allows end users to (i) execute and manage otherwise complex…

The web portal allows end users to (i) execute and manage otherwise complex command-line programs, (ii) launch multiple exploratory analyses of parameter-rich and computationally intensive methods…

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HTSeq
Desktop

HTSeq

A Python library to facilitate the rapid development of scripts. HTSeq offers…

A Python library to facilitate the rapid development of scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates,…

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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,…

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BioJava
Desktop

BioJava

An open-source project for processing of biological data in the Java…

An open-source project for processing of biological data in the Java programming language.

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BioPerl
Desktop

BioPerl

A community effort to produce Perl code which is useful in biology.

A community effort to produce Perl code which is useful in biology.

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Biopython
Desktop

Biopython

A set of freely available tools for biological computation written in Python by…

A set of freely available tools for biological computation written in Python by an international team of developers.

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Bpipe
Desktop

Bpipe

A dedicated programming language for defining and executing bioinformatics…

A dedicated programming language for defining and executing bioinformatics pipelines.

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Nestly
Desktop

Nestly

A Python package to facilitate running tools with nested combinations of…

A Python package to facilitate running tools with nested combinations of parameters and inputs.

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NGSANE
Desktop

NGSANE Next Generation Sequencing Analysis for Enterprises

A Linux-based, High Performance Computing (HPC) enabled framework that…

A Linux-based, High Performance Computing (HPC) enabled framework that minimises overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing…

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Moa
Desktop

Moa

Aims to assist a bioinformatician to organize, document, share, execute and…

Aims to assist a bioinformatician to organize, document, share, execute and repeat workflows in a command line environment without losing any of the flexibility of the command line.

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SeqPipe
Desktop

SeqPipe

A command line-based pipeline framework for bioinformatics research.

A command line-based pipeline framework for bioinformatics research.

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FastaValidator
Desktop

FastaValidator

A parser for the FASTA file format, which is one of the most common file…

A parser for the FASTA file format, which is one of the most common file formats to store nucleotide or protein sequence information.

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