Bioinformatics GitHub Repositories (2026) · Open Source Tools

Library for Digital Pathology Image Processing

Single-cell perturbation analysis

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

SortMeRNA: next-generation sequence filtering and alignment tool

Source code for JBrowse 2, a modern React-based genome browser

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

Official repo of the modular BioExcel version of HADDOCK

A cool place to store your Hi-C

A visualization grammar and GPU-accelerated toolkit for genomic data

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

A structural variation pipeline for short-read sequencing

Py3plex - A multilayer complex network visualization and analysis library in python3

R inside Python

Genomics Extension for SQLite

A genome diagram generator for microbes and organelles

Data visualisation web components for the life sciences.

Analyze your RNA sequencing data without writing a single line of code

A universal infrastructure layer for generative biology

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering