bedtools - the swiss army knife for genome arithmetic

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

Foundation Models for Genomics & Transcriptomics

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.

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

Official code repository for GATK versions 4 and up

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

The second version of the Kraken taxonomic sequence classification system

Official git repository for Biopython (originally converted from CVS)

C library for high-throughput sequencing data formats

A comprehensive library for computational molecular biology

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

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

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.