×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

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…
G T A T C G C T A
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.

G T A T C G C T A
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,…

G T A T C G C T A
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…

G T A T C G C T A
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,…

G T A T C G C T A
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…

G T A T C G C T A
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.

G T A T C G C T A
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…

G T A T C G C T A
Bpipe
Desktop

Bpipe

A dedicated programming language for defining and executing bioinformatics…

A dedicated programming language for defining and executing bioinformatics pipelines.

CLOUD
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.

G T A T C G C T A
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…

CLOUD
BioPig
Desktop

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
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…

G T A T C G C T A
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.

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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,…

G T A T C G C T A
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,…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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.

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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,…

G T A T C G C T A
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.

G T A T C G C T A
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.

G T A T C G C T A
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…

G T A T C G C T A
bx-python
Desktop

bx-python

Allows a rapid implementation of genome scale analyses. bx-python is a library…

Allows a rapid implementation of genome scale analyses. bx-python is a library containing a variety of useful modules. It can classify reading and working with genome-scale multiple local alignments.…

G T A T C G C T A
APIGenome
Desktop

APIGenome

Consists of a collection of libraries and command-line utilities for big data…

Consists of a collection of libraries and command-line utilities for big data genomics analysis. APIGenome is a package that started as a personal repository of small genomic analysis tools. It…

G T A T C G C T A
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…

G T A T C G C T A
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…

G T A T C G C T A
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.

G T A T C G C T A
SeqPipe
Desktop

SeqPipe

A command line-based pipeline framework for bioinformatics research.

A command line-based pipeline framework for bioinformatics research.

G T A T C G C T A
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,…

G T A T C G C T A
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.

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.