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Libraries/frameworks | High-throughput sequencing

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…
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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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EMBOSS
Desktop

EMBOSS European Molecular Biology Open Software Suite

Gives access to many free software tools for sequence analysis. EMBOSS aims to…

Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit.…

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GenomeSpace
Dataset

GenomeSpace

Represents a cloud-based and cooperative community resource. GenomeSpace…

Represents a cloud-based and cooperative community resource. GenomeSpace contains a large collection of bioinformatics tools. It allows seamless transition between tools and the large set of…

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Sleipnir
Desktop

Sleipnir

Allows to manipulate and mine very large biological data collections for…

Allows to manipulate and mine very large biological data collections for computational functional genomics. Sleipnir can perform common tasks: microarray processing, Bayesian and support vector…

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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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SMS
Web

SMS The Sequence Manipulation Suite

Allows analysis and manipulation of sequence data. SMS can display the genetic…

Allows analysis and manipulation of sequence data. SMS can display the genetic code, restriction enzyme set and codon usage table it uses that allowing users to make changes before performing an…

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blend4php
Desktop

blend4php

Offers a partial implementation of the Galaxy API and includes support for…

Offers a partial implementation of the Galaxy API and includes support for datasets, data types, folder contents, folders, genomes, group roles, groups, group users, histories, history contents,…

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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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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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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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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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Bpipe
Desktop

Bpipe

A dedicated programming language for defining and executing bioinformatics…

A dedicated programming language for defining and executing bioinformatics pipelines.

Eoulsan
Desktop

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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Rust-Bio
Desktop

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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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.

BioPig
Desktop

BioPig

Allows to analyze genomic data using Apache Pig and Hadoop. BioPig is built on…

Allows to analyze genomic data using Apache Pig and Hadoop. BioPig is built on MapReduce and Hadoop and thus has both the scalability and robustness offered by Apache Hadoop, and the programmability…

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SRSFseq
Desktop

SRSFseq Square Root Slope Functions sequencing

Allows users to analyze Illumina sequencing data. SRSFseq is made for analyzing…

Allows users to analyze Illumina sequencing data. SRSFseq is made for analyzing genomics data based on second-generation sequencing. The method of this tool permits researchers to interpret the…

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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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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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LATITUDES Network
Web

LATITUDES Network Library of Assessment Tools and InsTruments Used to assess Data validity in Evidence Syntheses

Improves the process of quality assessment in systematic reviews. LATITUDES…

Improves the process of quality assessment in systematic reviews. LATITUDES Network allows the development of quality assessment tools. It provides different tools for: (1) diagnostic accuracy…

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FireCloud
Web

FireCloud

Facilitates collaboration and enables reproducible science by providing a…

Facilitates collaboration and enables reproducible science by providing a robust, secure and scalable platform to the community at large. FireCloud is a NCI Cloud Pilot that provides a cancer genome…

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Euplotid
Desktop

Euplotid

Provides a set of bioinformatic pipelines, running in Docker, for building and…

Provides a set of bioinformatic pipelines, running in Docker, for building and annotating the local regulatory structure of genes. Euplotid is a linux based platform that can be used to make…

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SnakeChunks
Desktop

SnakeChunks

Offers shared code for the analysis of Next Generation Sequencing (NGS) data…

Offers shared code for the analysis of Next Generation Sequencing (NGS) data related to gene regulation: ChIP-seq, RNA-seq, and related technologies. SnakeChunks provides a collection of modular…

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Butler
Desktop

Butler

Enables scientific analysis on multiple cloud platforms. Butler includes four…

Enables scientific analysis on multiple cloud platforms. Butler includes four sub-systems which provide a way for (i) create and tears down clusters on several clouds, including defining Virtual…

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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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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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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
Desktop

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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Yabi
Desktop

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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Fastr
Desktop

Fastr

Creates and manages processing pipelines. Fastr is an image processing workflow…

Creates and manages processing pipelines. Fastr is an image processing workflow framework that speeds up the development cycle for creating workflows and minimizes the introduction of errors. The…

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Sequana
Desktop

Sequana

Provides a set of flexible genomic pipelines for processing and reporting Next…

Provides a set of flexible genomic pipelines for processing and reporting Next Generation Sequencing (NGS) analysis. Sequana contains also some standalone applications: 1) sequana_coverage eases the…

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BioPerl
Desktop

BioPerl

Manages and manipulates life-science information. Bioperl provides an…

Manages and manipulates life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. It is capable of executing…

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Bioclojure
Desktop

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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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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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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PyBrain
Desktop

PyBrain

Facilitates both the application of and research on premier learning…

Facilitates both the application of and research on premier learning algorithms. PyBrain is a machine learning library that implements many recent learning algorithms and architectures ranging from…

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PAW
Desktop

PAW Physics Analysis WorkStation

Supports researchers in data presentation and analysis by using some components…

Supports researchers in data presentation and analysis by using some components from the CERN Program Library. PAW supplies an interface which allows users to build graphical presentation or express…

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BioCocoa
Desktop

BioCocoa

Offers reusable OpenStep classes that are specially designed for molecular…

Offers reusable OpenStep classes that are specially designed for molecular biology and bioinformatics. BioCocoa permits to design biological sequences that are powerful and lightweight. It provides…

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Bionode.io
Desktop

Bionode.io

Offers tools to make bioinformatic analysis. Bionode permits to construct…

Offers tools to make bioinformatic analysis. Bionode permits to construct complex and reproducible pipelines. It allows users to track versions and changes for each software available on the tool.

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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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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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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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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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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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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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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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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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GEMBASSY
Web
Desktop

GEMBASSY

Offers a toolkit encompassing more than 50 tools for genome analysis and…

Offers a toolkit encompassing more than 50 tools for genome analysis and gene-centric sequence manipulation. GEMBASSY compiles applications issued from the G-language web services and is available as…

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