Gatk alternatives for AI agents.

Data intensive science for everyone.

Java utilities for Bioinformatics

Official git repository for Biopython (originally converted from CVS)

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Cloud-native genomic dataframes and batch computing

: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

A Go package for engineering organisms.

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

Python library to facilitate genome assembly, annotation, and comparative genomics