Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. — Wikipedia
A curated list of awesome Bioinformatics software, resources, and libraries. Mostly command line based, and free or open-source. Please feel free to contribute!
Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.
Bioperl - International association of users & developers of open source Perl tools for bioinformatics, genomics and life sciences. [ paper-2002 | web ]
Bioconductor - A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
Biopython - Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
Bioconda - A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with
conda install) bioinformatics packages. [ paper-2018 | web ]
BioJulia - Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
Rust-Bio - Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
SeqAn - The modern C++ library for sequence analysis.
(Poly)merase - A Go library and command line utility for engineering organisms.
Biocaml - Biocaml aims to be a high-performance user-friendly library for Bioinformatics.
Sequence Processing includes tasks such as demultiplexing raw read data, and trimming low quality bases.
The following items allow for scalable genomic analysis by introducing specialized databases.
blastxlike searches. [ paper-2021 ]
.bamfiles, used for testing mutation callers. [ web ]
The following tools can be used to visualize genomic data or for constructing customized visualizations of genomic data including sequence data from DNA-Seq, RNA-Seq, and ChIP-Seq, variants, and more.