Awesome Bioinformatics

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!

Table of Contents

• Package suites
• Data Tools
• Downloading
• Compressing
• Data Processing
• Command Line Utilities
• Next Generation Sequencing
• Workflow Managers
• Pipelines
• Sequence Processing
• Data Analysis
• Sequence Alignment
  • Pairwise
  • Multiple Sequence Alignment
  • Clustering
• Quantification
• Variant Calling
  • Structural variant callers
• BAM File Utilities
• VCF File Utilities
• GFF BED File Utilities
• Variant Simulation
• Variant Prediction/Annotation
• Python Modules
  • Data
  • Tools
• Assembly
• Annotation
• Long-read sequencing
• Long-read Assembly
• Visualization
• Genome Browsers / Gene Diagrams
• Circos Related
• Database Access
• Resources
• Becoming a Bioinformatician
• Bioinformatics on GitHub
• Sequencing
• RNA-Seq
• ChIP-Seq
• YouTube Channels and Playlists
• Blogs
• Miscellaneous
• Online networking groups
• License

---

Package suites

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.