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SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.

The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.

Ultra-fast, sensitive search and clustering suite for protein and nucleotide sequence sets.

A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

A Swiss Army knife for genome arithmetic.

BWA-MEM drop-in replacement: 2-3x faster, 2-5x cheaper, 100% identical output on standard CPUs.

lumpy: a general probabilistic framework for structural variant discovery.

Minigraph is a sequence-to-graph mapper and graph constructor. For graph generation, it aligns a query sequence against a sequence graph and incrementally augments an existing graph with long query subsequences diverged from the graph.

Toolkit for processing sequences in FASTA/Q formats.

Standalone C library for assembling Illumina short reads in small regions

A wee tool for random access into BGZF files.