Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundrynpx agentmods add skills/ma-compbio-lab/skillfoundry/minimap2-read-mapping-starterWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/minimap2-read-mapping-starter)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/minimap2-read-mapping-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/minimap2-read-mapping-starter/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/minimap2-read-mapping-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/minimap2-read-mapping-starter.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00000 | $0.00315 |
| Opus 5 | $0.00000 | $0.00158 |
| Sonnet 5 | $0.00000 | $0.00063 |
| Haiku 4.5 | $0.00000 | $0.00032 |
Grade A, and why
minimap2-read-mapping-starter scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
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 srfrom 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"]
What ships with it
9 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- assets/toy_reads_mapping_summary.json 1006 B
- assets/toy_reads.bam 535 B
- assets/toy_reads.bam.bai 96 B
- examples/toy_reads.fastq 324 B
- examples/toy_reference.fa 104 B
- metadata.yaml 1.4 KB
- refs.md 276 B
- scripts/run_minimap2_read_mapping.py 4.9 KB runs code
- tests/test_run_minimap2_read_mapping.py 2.5 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 5d ago First seen · 31 lines · 0 tokens per session scan A 5f00089f6df7
minimap2-read-mapping-starter is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It costs nothing until one of its globs matches a file; then it loads 315 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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