bioinformatics

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Specification for the Workflow Description Language (WDL).

The next version of bwa-mem

Python package for graph neural networks in chemistry and biology

Plant phenotyping with image analysis

A fast and sensitive gapped read aligner

Bioinformatics containers

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

Precision Medicine Knowledge Graph (PrimeKG)

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Tools to process and analyze deep sequencing data.

Annotated data.

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

Working with molecular structures in pandas DataFrames

Versatile open-source tool for microbiome analysis

A Go package for engineering organisms.

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

A high-performance, Pythonic language for bioinformatics

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

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

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

Structural variation caller using third generation sequencing

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

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

Gene cluster comparison figure generator

A scikit-learn compatible library for graph kernels

BWK awk modified for biological data

Remote protein homology detection suite.

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

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

Tools for working with SAM/BAM data

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

Signal-level algorithms for MinION data

Yet another redundant workflow engine

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

The Chemistry Development Kit

Biostar Q&A

Cutadapt removes adapter sequences from sequencing reads

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.

Open-source bioinformatics components for Dash

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

BioMCP: Biomedical Model Context Protocol

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

An analysis and visualization platform for 'omics data

d3 library to build circular graphs

Java utilities for Bioinformatics