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 agentmods add skills/tiangzlab/omicsclaw/genomics-assemblynpx skills add TianGzlab/OmicsClaw --skill genomics-assemblygit clone --depth 1 https://github.com/TianGzlab/OmicsClawWrote 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/tiangzlab/omicsclaw/genomics-assembly)<a href="https://agentmods.dev/skills/tiangzlab/omicsclaw/genomics-assembly"><img src="https://agentmods.dev/badge/skills/tiangzlab/omicsclaw/genomics-assembly.svg" alt="Measured on agentmods" 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 | $0.00077 | $0.01032 |
| Opus 5 | $0.00039 | $0.00516 |
| Sonnet 5 | $0.00015 | $0.00206 |
| Haiku 4.5 | $0.00008 | $0.00103 |
Grade A, and why
genomics-assembly 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.
How it starts
The opening of the file, as written. The whole thing — 88 lines — stays where its author put it; the contents beside it link to each section on GitHub.
genomics-assembly
When to use
The user has a FASTA from any de novo assembler (SPAdes, Megahit,
Flye, Canu, etc.) and wants standard QUAST-compatible quality
metrics: contig count, N50 / N90, L50 / L90, total length, longest
contig, GC content, optional completeness fraction (when
--genome-size is provided).
This skill does NOT run the assembly. It consumes the FASTA the assembler emits.
Inputs & Outputs
Inputs
- File types:
.fasta,.fa
Outputs
tables/assembly_metrics.csvtables/contig_lengths.csvreport.mdresult.json
Flow
- Load FASTA (
--input <assembly.fasta>) or generate a demo assembly atoutput_dir/demo_assembly.fasta(genome_assembly.py:186). - Parse contigs (
genome_assembly.py:52-67); each line is uppercased on read so case is normalised. - Sort by length; compute cumulative N50 / N90 / L50 / L90 + total / longest + assembly-wide GC% from concatenated sequence.
- If
--genome-sizeis set and > 0, computecompleteness_pct = total_length / genome_size * 100. - Write
tables/contig_lengths.csv(genome_assembly.py:309) +tables/assembly_metrics.csv(:312) +report.md+result.json.
Gotchas
- No assembler is invoked. This skill summarises an existing FASTA — it does not run SPAdes / Megahit / Flye / Canu. Run them upstream and feed the resulting FASTA here.
--inputREQUIRED unless--demo.genome_assembly.py:290raisesValueError("--input required when not using --demo"); non-existent paths raiseFileNotFoundErrorat:293.--genome-size 0(default) skips completeness. Without an expected genome size (genome_assembly.py:279, default 0), the report omits the completeness column entirely. Pass--genome-size 3000000000for a human-scale assembly to populate it.- Soft-masked bases are normalised to uppercase before GC counting.
genome_assembly.py:67callsline.upper()per FASTA line, so lowercase soft-masked regions contribute identically to hard-masked / unmasked sequence in the GC%. There is no way to exclude soft-masked regions short of pre-filtering the FASTA. - Demo FASTA has 100 contigs of varying length.
--demowrites a fixed-pattern synthetic file useful for orchestrator smoke tests; the N50 it produces is not biologically meaningful.
What ships with it
5 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.
- 5d ago First seen · 88 lines · 77 tokens per session scan A e3f2ff71bd51
genomics-assembly is a skill published in the GitHub repository TianGzlab/OmicsClaw (160 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 77 tokens to every session and 1,032 once invoked, about $0.0004 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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