LiteratureScientific Writing & PublishingFreedomIntelligence/OpenClaw-Medical-SkillsLiterature Review

bio-longread-alignment

Maintainer FreedomIntelligence · Last updated April 1, 2026

Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.

OpenClawNanoClawDiscoveryReadingbio-longread-alignment🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcalign

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-alignment

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: minimap2 -ax map-ont ref.fa reads.fq | samtools sort -o aligned.bam (ONT), minimap2 -ax map-hifi (PacBio HiFi).
Align my long reads to the reference" → Map ONT or PacBio reads using minimap2 with technology-specific presets for optimal sensitivity and accuracy. CLI: minimap2 -ax map-ont ref.fa reads.fq | samtools sort -o aligned.bam (ONT), minimap2 -ax map-hifi (PacBio HiFi).
minimap2 -ax map-ont reference.fa reads.fastq.gz | \ samtools sort -o aligned.bam samtools index aligned.bam.

Source Doc

Excerpt From SKILL.md

PacBio HiFi reads (high accuracy)

minimap2 -ax map-hifi reference.fa reads.fastq.gz |
samtools sort -o aligned.bam samtools index aligned.bam


## PacBio CLR (continuous long reads, lower accuracy)

minimap2 -ax map-pb reference.fa reads.fastq.gz | \
    samtools sort -o aligned.bam
samtools index aligned.bam