#bioinformatics

Python script to upload bins and MAGs to ENA (European Nucleotide Archive)

This Python package contains a collection of scripts and tools for including in MGnify pipelines

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

The Pharmacogenomic Clinical Annotation Tool

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

Embeddable genomic visualization component based on the Integrative Genomics Viewer

JAMMA (Highly-Accelerated Multi-method Mixed-model Association) -- a fast and modern Python and C reimplementation of GEMMA for large-scale GWAS.

PDBe MCP Servers integrate Protein Data Bank Europe resources with LLMs via Model Context Protocol. Provides seamless access to protein structure data through API tools and graph database schema assistance for intelligent Cypher query generation, bridging structural biology and AI research.

A hybrid assembly and MAG recovery pipeline (and more!)

Search ClinicalTrials.gov trials, retrieve study details and results, and match patients to eligible trials via MCP. STDIO or Streamable HTTP.

Making Protein folding accessible to all!

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

cython + htslib == fast VCF and BCF processing

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

Python Ensembl code source repository

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

SortMeRNA: next-generation sequence filtering and alignment tool

Yet another version of PDBx/mmCIF Python implementation