minimap2

name	minimap2
description	Fast pairwise alignment for long reads and genome-to-genome maps. Use this skill when working with minimap2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/lh3/minimap2. For stage routing use tool-selection / metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["mapping","alignment","long-read"]
upstream	https://github.com/lh3/minimap2
stage	mapping

Minimap2

Upstream: Minimap2

Citation

Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018). https://doi.org/10.1093/bioinformatics/bty191

See also docs/references.md.

Analytical thinking

Use for ONT/PacBio→assembly (map-ont/map-hifi) and assembly polishing/scaffolding maps. Not the first choice for Illumina→contig coverage (prefer Bowtie2/BWA/strobealign).

How to run

conda install -c bioconda minimap2  # if packaged; else follow upstream

minimap2 -ax map-ont -t 16 contigs.fa reads.fastq.gz \
  | samtools sort -@ 8 -o temp/map/lr.bam
# HiFi: -ax map-hifi
# short vs short assembly splice-unaware: -ax sr

Key parameters

| -ax map-ont | ONT | | | -ax map-hifi | PacBio HiFi | | | -ax sr | short reads | OK but Bowtie2/BWA often preferred |

Decision notes

• Stage: mapping (long reads / genome-to-genome)
• Prefer for ONT/PacBio→contigs and assembly polish maps; not default Illumina coverage mapper

Related skills

bowtie2 · bwa · metaflye · metamdbg · samtools · tool-selection · metagenomics-workflow