lh3/minimap2

Health v2 · maintenance only

Flags: no_license

Adoption not part of the score

2242 stars · 475 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

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

cli-tool · maturity stable

search-engine developer-tools bioinformatics windows cli python sequence-alignment genomics spliced-alignment long-reads bioinformatics python-binding linux macos

Member repositories

For agents

markdown · JSON · MCP: product_card(name="lh3/minimap2")