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…
Desktop app
G T A T C G C T A Snakemake Snakemake

Snakemake

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

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

CLOUD Eoulsan Eoulsan

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.

CLOUD BioPig BioPig

BioPig

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

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

G T A T C G C T A Yabi Yabi

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…

Desktop app
G T A T C G C T A MolBioLib MolBioLib

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.

Desktop app
G T A T C G C T A VisRseq VisRseq

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…

Desktop app
G T A T C G C T A SeqAn SeqAn

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…

Desktop app
G T A T C G C T A htslib htslib

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…

Desktop app
G T A T C G C T A Bioconductor Bioconductor

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,…

G T A T C G C T A Bioclojure Bioclojure

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…

Desktop app
G T A T C G C T A Support Users for… Support Users for SHell-script Integration

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…

Desktop app
G T A T C G C T A GenOO GenOO

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…

G T A T C G C T A Rust-Bio Rust-Bio

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…

Desktop app
G T A T C G C T A CracTools CracTools

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…

Desktop app
G T A T C G C T A BioJS BioJS

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…

Desktop app
G T A T C G C T A Ruby Bioinformatics… Ruby Bioinformatics Toolkit

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…

Desktop app
G T A T C G C T A Whiteboard Whiteboard

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…

Desktop app
G T A T C G C T A Ruffus Ruffus

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…

Desktop app
G T A T C G C T A BioRuby BioRuby

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,…

Web app
G T A T C G C T A Mobyle SNAP Workbench Mobyle SNAP Workbench

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…

Desktop app
G T A T C G C T A HTSeq HTSeq

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,…

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 BioJava BioJava

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.

Desktop app
G T A T C G C T A BioPerl BioPerl

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.

Desktop app
G T A T C G C T A Biopython Biopython

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.

Desktop app
G T A T C G C T A Bpipe Bpipe

Bpipe

A dedicated programming language for defining and executing bioinformatics…

A dedicated programming language for defining and executing bioinformatics pipelines.

Desktop app
G T A T C G C T A Nestly Nestly

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.

Desktop app
G T A T C G C T A Next Generation… Next Generation Sequencing Analysis for…

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…

Desktop app
G T A T C G C T A Moa Moa

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.

Desktop app
G T A T C G C T A SeqPipe SeqPipe

SeqPipe

A command line-based pipeline framework for bioinformatics research.

A command line-based pipeline framework for bioinformatics research.

Desktop app
G T A T C G C T A i2x i2x

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,…

Desktop app
G T A T C G C T A FastaValidator FastaValidator

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.

Desktop app
G T A T C G C T A Hail Hail

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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