Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add zongtingwei/Bioclaw_Skills_Hub --skill alignment-and-mappinggit clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_HubWrote 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/zongtingwei/bioclaw_skills_hub/alignment-and-mapping)<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/alignment-and-mapping"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/alignment-and-mapping/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/zongtingwei/bioclaw_skills_hub/alignment-and-mapping"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/alignment-and-mapping.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 | $0.00023 | $0.00869 |
| Opus 5 | $0.00012 | $0.00434 |
| Sonnet 5 | $0.00005 | $0.00174 |
| Haiku 4.5 | $0.00002 | $0.00087 |
Grade A, and why
alignment-and-mapping 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 12d 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.
How it starts
The opening of the file, as written. The whole thing — 139 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Alignment And Mapping
Version Compatibility
Reference examples assume recent stable releases of the preferred tools, especially samtools and the other tools listed below.
Before using code or command patterns, verify installed versions match the environment:
- Python:
python -c "import <module>; print(<module>.__version__)" - CLI:
<tool> --version - If signatures differ, inspect the installed help or API and adapt the pattern instead of retrying unchanged.
Overview
Workflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.
When To Use This Skill
- use when the task is sequence alignment or alignment file preparation
- use when FASTQ files must be mapped to a genome or transcriptome
- use when BAM or CRAM files and mapping metrics are the expected outputs
Quick Route
- If the input is raw or minimally processed data, start with validation and QC before any modeling.
- If the input is already processed, skip directly to the first workflow step that matches the user goal.
- If the user asks for a biological conclusion, always produce at least one QC or confidence artifact alongside the final result.
Progressive Disclosure
- Read
references/technical_reference.mdwhen you need deeper tool-selection rules, environment adaptation notes, or extra validation guidance. - Keep
SKILL.mdas the main execution path and load the reference file only when the task or failure mode needs the extra detail.
Default Rules
- Prefer Python-first workflows unless the task explicitly requires something else.
- Keep intermediate and final outputs separated.
- Record software versions, reference builds, and key parameters when they affect interpretation.
- Favor reproducible tables and figures over one-off interactive-only outputs.
Expected Inputs
- FASTQ files
- reference genome or transcriptome
- alignment indexes
Expected Outputs
- sorted and indexed alignments
- mapping metrics
- downstream-ready BAM or CRAM files
What ships with it
2 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.
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.
- 12d ago First seen · 139 lines · 23 tokens per session scan A 7ec307781e3b
alignment-and-mapping is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (26 stars, last pushed 5mo ago), licensed MIT. It adds 23 tokens to every session and 869 once invoked, about $0.0001 per session on Opus 5. 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 2026-08-30.
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