minimap2

Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.

homepage: https://github.com/lh3/minimap2

Available installations

minimap2 version	Supported CPU targets	Supported GPU targets	EESSI version	Module
2.30	generic: aarch64, x86_64 Arm: a64fx, neoverse_n1, neoverse_v1, nvidia/grace AMD: zen2, zen3, zen4 Intel: haswell, skylake_avx512, sapphirerapids, icelake, cascadelake	(none)	2025.06	minimap2/2.30-GCCcore-14.3.0