| 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.
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| 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
minimap2 -ax map-ont -t 16 contigs.fa reads.fastq.gz \
| samtools sort -@ 8 -o temp/map/lr.bam
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
