Jvarkit alternatives for AI agents.

Official code repository for GATK versions 4 and up

Data intensive science for everyone.

The Chemistry Development Kit

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

Scripts to download genomes from the NCBI FTP servers

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Tools to process and analyze deep sequencing data.

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.

Plant phenotyping with image analysis

A fast and sensitive gapped read aligner

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Official git repository for Biopython (originally converted from CVS)

Making Protein folding accessible to all!

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