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

• Skill-local tests: python3 -m unittest discover -s skills/genomics/minimap2-read-mapping-starter/tests -p 'test_*.py'
• Expected summary: read_count == 3, mapped_count == 2, reference_names == ["chrToy"]