Adam alternatives for AI agents.

Official git repository for Biopython (originally converted from CVS)

Cloud-native genomic dataframes and batch computing

Scripts to download genomes from the NCBI FTP servers

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

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Official code repository for GATK versions 4 and up

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

Data intensive science for everyone.

Java utilities for Bioinformatics

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

A full spaCy pipeline and models for scientific/biomedical documents.

Tools to process and analyze deep sequencing data.

A comprehensive library for computational molecular biology

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.