Claw Metagenomics

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “/claw-metagenomics”

Requirements

• Python 3

Workflow steps

9 steps, taken from the first numbered list in SKILL.md.

1. 1Takes paired-end FASTQ files (R1, R2) or a single concatenated FASTQ as input
2. 2Runs Kraken2 taxonomic classification against a standard database (e.g., Standard-8, PlusPF)
3. 3Refines abundances with Bracken at species level (read re-estimation)
4. 4Detects antimicrobial resistance genes with RGI against the CARD database
5. 5Classifies detected ARGs by WHO critical priority pathogen association
6. 6Optionally runs HUMAnN3 for functional pathway profiling (MetaCyc + UniRef)
7. 7Calculates alpha diversity metrics from Bracken-adjusted species abundances
8. 8Generates four publication-quality figures
9. 9Produces a full reproducibility bundle (commands.sh, environment.yml, checksums.sha256)

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Claw Metagenomics loads about 2.4k tokens when it runs. Until then it costs about 24 tokens; SKILL.md has 650 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~24

When it runs · the whole SKILL.md, loaded when a task matches

~2.4k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 650 words, ~2,412 tokens.

name

claw-metagenomics

description

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

license

MIT

metadata.version

0.1.0

metadata.author

Manuel Corpas

metadata.tags

metagenomics, antimicrobial-resistance, taxonomy, functional-profiling, environmental, WHO-critical-ARGs

# Full pipeline (taxonomy + resistome + functional)
python metagenomics_profiler.py \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --output metagenomics_report

# Skip HUMAnN3 (faster — taxonomy + resistome only)
python metagenomics_profiler.py \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --output metagenomics_report \
    --skip-functional

# Single concatenated FASTQ
python metagenomics_profiler.py \
    --input combined.fastq.gz \
    --output metagenomics_report

# Specify Kraken2 database path
python metagenomics_profiler.py \
    --r1 sample_R1.fastq.gz \
    --r2 sample_R2.fastq.gz \
    --output metagenomics_report \
    --kraken2-db /path/to/kraken2_db \
    --read-length 150

python metagenomics_profiler.py --demo --output demo_report

Metagenomics Profiler — ClawBio
================================
Mode: demo (pre-computed Peru sewage data)
Samples: 6 (3 sites: Lima, Cusco, Iquitos)

Taxonomy (Kraken2 + Bracken):
  Total classified: 94.2%
  Top species: Escherichia coli (12.3%), Klebsiella pneumoniae (8.7%),
               Pseudomonas aeruginosa (5.1%), Acinetobacter baumannii (3.9%)

Alpha Diversity:
  Shannon index: 2.847
  Simpson index: 0.912
  Pielou evenness: 0.734
  Species richness: 48

Resistome (RGI/CARD):
  Total ARG hits: 247 (Perfect: 89, Strict: 158)
  Drug classes: 14
  WHO-Critical ARGs detected: 23
    - Carbapenem resistance: NDM-1, OXA-48, KPC-3
    - 3rd-gen cephalosporin resistance: CTX-M-15, CTX-M-27

Functional Pathways (HUMAnN3):
  Total pathways: 312
  Top: PWY-7219 (adenosine ribonucleotides de novo biosynthesis)

Figures saved to: demo_report/figures/
  taxonomy_barplot.png (300 dpi)
  resistome_heatmap.png (300 dpi)
  who_critical_args.png (300 dpi)

Reproducibility:
  commands.sh | environment.yml | checksums.sha256

FASTQ R1 + R2
     |
     v
[Kraken2] --> kraken2_report.txt
     |
     v
[Bracken] --> bracken_species.tsv   --> Figure 1: Taxonomy bar chart
     |
     v
[RGI MAIN] --> rgi_results.txt      --> Figure 2: Resistome heatmap
     |                                --> Figure 3: WHO-critical ARG summary
     v
[HUMAnN3] --> pathabundance.tsv     (optional, --skip-functional to omit)
     |
     v
[Report] --> report.md + figures/ + reproducibility/

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file in skills/claw-metagenomics of ClawBio/ClawBio.

• SKILL.md
• metagenomics_profiler.py

Open the folder on GitHubat commit dece754

Used in 3 other repositories

We found 3 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 3 other GitHub owners. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

• aAAaqwq/AGI-Super-Teamskills/claw-metagenomics
• FreedomIntelligence/OpenClaw-Medical-Skillsskills/claw-metagenomics
• BioTender-max/awesome-bio-agent-skillsskills/clawbio/claw-metagenomics