bioinformatics

Python and C++ code for reading and writing genomics data.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Bioinformatics containers

A fast and sensitive gapped read aligner

Plant phenotyping with image analysis

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Tools to process and analyze deep sequencing data.

Working with molecular structures in pandas DataFrames

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

🦖 ClawBio — The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Built on OpenClaw.

Versatile open-source tool for microbiome analysis

Precision Medicine Knowledge Graph (PrimeKG)

Annotated data.

A Go package for engineering organisms.

Ultra-fast and memory-efficient (meta-)genome assembler

A high-performance, Pythonic language for bioinformatics

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al....

Structural variation caller using third generation sequencing

A scikit-learn compatible library for graph kernels

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

BWK awk modified for biological data

Gene cluster comparison figure generator

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Remote protein homology detection suite.

Tools for working with SAM/BAM data

🔬🦞 A self-evolving AI research colleague for scientists. 285 skills, zero hallucination, persistent memory.

Signal-level algorithms for MinION data

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Biostar Q&A

Yet another redundant workflow engine

The Chemistry Development Kit

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Cutadapt removes adapter sequences from sequencing reads

Open-source bioinformatics components for Dash

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

COBRApy is a package for constraint-based modeling of metabolic networks.

Accurate sample inference from amplicon data with single nucleotide resolution

Quickly search, compare, and analyze genomic and metagenomic data sets.

React component for Cytoscape.js network visualisations

d3 library to build circular graphs

ScienceClaw is a personal research assistant built with LangChain DeepAgents and AIO Sandbox infrastructure, adopting a completely new architecture be...

Java utilities for Bioinformatics

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http...

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

An analysis and visualization platform for 'omics data

A curated list of resources for learning bioinformatics.