Minimap2 read mapping starter

Skill ma-compbio-lab/SkillFoundry/skills/genomics/minimap2-read-mapping-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill minimap2-read-mapping-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.3 KB, 313 tokens by cl100k_base, as published. Nobody here has run it

minimap2 Read Mapping Starter

Use this skill to align a tiny FASTQ file against a small reference with minimap2, sort and index the resulting BAM, and summarize the alignments.

What it does

runs minimap2 -a -x sr from the repo-managed genomics prefix
sorts and indexes the alignment with samtools
reports mapped and unmapped reads, mean MAPQ, and representative alignments

When to use it

you need a verified starter for alignment-and-mapping
you want a minimal short-read mapping example before adding quantification or variant calling
you need a deterministic BAM-producing smoke fixture

Example

./slurm/envs/genomics/bin/python skills/genomics/minimap2-read-mapping-starter/scripts/run_minimap2_read_mapping.py \
  --reference skills/genomics/minimap2-read-mapping-starter/examples/toy_reference.fa \
  --reads skills/genomics/minimap2-read-mapping-starter/examples/toy_reads.fastq \
  --bam-out scratch/genomics/minimap2/toy_reads.bam \
  --summary-out scratch/genomics/minimap2/toy_reads_summary.json

Verification