# lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Repository: https://github.com/lh3/minimap2
Canonical: https://ross.abutalabs.com/products/minimap2
Homepage: https://lh3.github.io/minimap2
Language: C
License: NOASSERTION
License Family: other
Topics: bioinformatics, sequence-alignment, spliced-alignment, genomics
Last push: 2026-05-19T22:40:40+00:00

## Health v2 (maintenance only)
Score: 76/100 (v2, computed 2026-09-03T02:20:16.233290+00:00)
- activity 83, release rhythm 52, longevity 100
- inputs: {"age_days": 3333, "days_push": 106, "days_rel": 106, "gap_med": 198.0, "n_releases_24m": 3}
- flags: no_license
- formula: round(0.45*activity + 0.35*rhythm + 0.20*longevity); archived -> min(score, 10)

## Adoption (not part of the score)
Stars 2242, forks 475 (observed 2026-08-28T04:06:29.775360+00:00)

## What it is
minimap2 is a fast, versatile pairwise sequence aligner for genomic and spliced (RNA-seq) nucleotide sequences, written in C. It maps long noisy reads (PacBio, Oxford Nanopore), short reads, and assembles against reference genomes, outputting SAM/PAF alignments.

## Use cases
- align long nanopore reads to a reference genome
- map PacBio HiFi reads to a genome
- align RNA-seq reads across splice junctions
- find overlaps between long reads for assembly
- align two genome assemblies to each other
- map short paired-end Illumina reads
- index a reference genome for fast repeated mapping

## When to choose
- you need to align long noisy sequencing reads to a reference genome
- you need spliced alignment for RNA-seq or direct RNA reads
- you need fast whole-genome or assembly-to-assembly alignment
- you want a fast, memory-efficient alternative to BWA for long reads

## When to avoid
- you need base-level variant calling with statistical scoring models
- you need protein or translated alignment
- you need a graphical interface for alignment tasks

## Facets
- artifact type: cli-tool
- maturity: stable
- function: search-engine, developer-tools
- domain: bioinformatics
- platform: windows, cli, python
- tags: sequence-alignment, genomics, spliced-alignment, long-reads, bioinformatics, python-binding, linux, macos

## Member repositories
- lh3/minimap2 (main) score 76

## Provenance
- Observed fields: from GitHub, fetched 2026-08-28T04:06:29.775360+00:00.
- Health v2: computed from the inputs above; adoption is never an input.
- Inferred fields (summary, facets, guidance): AI-extracted, prompt v1, taxonomy v1, on 2026-08-30T02:44:04.574729+00:00, confidence not recorded.
  - readme: https://github.com/lh3/minimap2 (fetched 2026-08-28T04:06:29.775360+00:00, sha 1329706e0d88)
  - homepage: https://lh3.github.io/minimap2 (fetched 2026-08-29T10:24:19.526885+00:00, sha dc75e3341224)
- Data as of 2026-08-30T08:39:29.467469+00:00.