Bioinformatics GitHub Repositories (2026) · Open Source Tools

The open-source AI workbench for scientific research

Single-cell analysis in Python. Scales to >100M cells.

Open-source, local-first desktop AI research workbench for scientific computing with Python/R, MCP bioinformatics tools, SSH/WSL/GPU runtimes, and OpenAI/Anthropic models.

A unifying framework for biomedical research knowledge graphs

Conda recipes for the bioconda channel.

BioMCP: Biomedical Model Context Protocol

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Differential analysis tool for coding-free researchers – instant statistical results and charts, ready for your lab meeting. Just unzip and run! No-coding!

Randomly subsample sequencing reads or alignments

Python package to perform enrichment analysis from omics data.

The Pharmacogenomic Clinical Annotation Tool

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Aggregate results from bioinformatics analyses across many samples into a single report.

Data Apps & Dashboards for Python. No JavaScript Required.

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Cloud-native genomic dataframes and batch computing

A comprehensive library for computational molecular biology

The Chemistry Development Kit

Genome viewer for you and your agents.

A tool to map bisulfite converted sequence reads and determine cytosine methylation states