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.

bedtools - the swiss army knife for genome arithmetic

Foundation Models for Genomics & Transcriptomics

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

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

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

IQ-TREE software version 2: phylogenetics by maximum likelihood

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

Official code repository for GATK versions 4 and up

Official git repository for Biopython (originally converted from CVS)

The second version of the Kraken taxonomic sequence classification system

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

A comprehensive library for computational molecular biology

C library for high-throughput sequencing data formats

Tools (written in C using htslib) for manipulating next-generation sequencing data

Oxford Nanopore's Basecaller

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.