{"added":null,"apiVersion":1,"behindSince":null,"buildDepends":[],"categories":["biology","python"],"comment":"Sequence alignment program for noisy, long reads","compare":"/compare/minimap2/index.json","dependentCount":null,"description":"Minimap2 is a versatile sequence alignment program that aligns DNA or\nmRNA sequences against a large reference database. Typical use cases\ninclude: (1) mapping PacBio or Oxford Nanopore genomic reads to the\nhuman genome; (2) finding overlaps between long reads with error rate\nup to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore\ncDNA or Direct RNA reads against a reference genome; (4) aligning\nIllumina single- or paired-end reads; (5) assembly-to-assembly\nalignment; (6) full-genome alignment between two closely related\nspecies with divergence below ~15%.\n\nFor ~10kb noisy reads sequences, minimap2 is tens of times faster than\nmainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and\nGMAP. It is more accurate on simulated long reads and produces\nbiologically meaningful alignment ready for downstream analyses. For\n\u003e100bp Illumina short reads, minimap2 is three times as fast as\nBWA-MEM and Bowtie2, and as accurate on simulated data.  Detailed\nevaluations are available from the minimap2 paper\n(https://doi.org/10.1093/bioinformatics/bty191).","flavors":[],"html":"https://daemonports.org/netbsd/biology/minimap2/","kind":"port","lastUpdate":null,"license":["mit"],"maintainer":"pkgsrc-users@NetBSD.org","name":"minimap2","newest":false,"newestVersion":"2.31","noVulnData":false,"origin":"biology/minimap2","otherSystems":[{"maintainer":"ports@FreeBSD.org","newest":true,"origin":"biology/minimap2","path":"/biology/minimap2/","system":"FreeBSD","updated":"2026-10-08","version":"2.31"},{"maintainer":"jwb@FreeBSD.org","origin":"biology/minimap2","path":"/dragonfly/biology/minimap2/","system":"DragonFly","version":"2.28_1"},{"maintainer":"jwb@FreeBSD.org","newest":true,"noVulnData":true,"origin":"biology/minimap2","path":"","system":"HardenedBSD","version":"2.31"},{"maintainer":"jwb@FreeBSD.org","newest":true,"noVulnData":true,"origin":"biology/minimap2","path":"","system":"GhostBSD","version":"2.31"}],"packages":[{"repo":"NetBSD 10.1 x86_64","versions":["2.28nb1"]},{"repo":"NetBSD 10.1 aarch64","versions":["-"]},{"repo":"SmartOS / illumos x86_64","versions":["2.28nb1"]},{"repo":"macOS 15 arm64","versions":["-"]}],"pkgName":"minimap2-2.28nb1","related":["wip/minimap2","wip/py-mappy"],"repository":"pkgsrc","requiredBy":["wip/biostar-tools"],"requiredByCount":1,"runDepends":[],"status":null,"system":"netbsd","systemLabel":"NetBSD","version":"2.28nb1","versions":null,"vulnerabilities":null,"www":"https://github.com/lh3/minimap2"}