Profile shotgun metagenomic FASTQ data for taxonomy, resistome, and pathways.
npx skills add https://github.com/ClawBio/ClawBio --skill claw-metagenomics
Please help me install this Agent Skill. Skill: claw-metagenomics Source: https://github.com/ClawBio/ClawBio/tree/main/skills/claw-metagenomics Command: npx skills add https://github.com/ClawBio/ClawBio --skill claw-metagenomics
Raw shotgun metagenomic reads are complex to configure and interpret: choosing correct taxonomic databases and thresholds, reliably detecting antimicrobial resistance genes without false positives, obtaining pathway-level functional context, and producing reproducible results are time-consuming and error-prone for researchers and public-health teams.
Run the metagenomics profiler on paired-end FASTQ to produce taxonomy, resistome, pathway reports, publication figures, and a reproducibility bundle.
High-intent search queries and answers about installing and using this skill.
Profile shotgun metagenomic sequencing data by running Kraken2 classification with Bracken species-level re-estimation and RGI against CARD for resistome detection. This generates species-level taxonomy, antimicrobial resistance gene detections, and functional pathway abundances from paired-end or single concatenated FASTQ files.
RGI resistome detection limits results to Perfect and Strict hits against the CARD database to minimize false positives. Detections are then mapped to WHO priority pathogen tiers, ensuring reliable antimicrobial resistance gene identification for clinical or environmental surveillance studies.
Kraken2 provides taxonomic profiling while optional HUMAnN3 generates functional pathway abundance using MetaCyc and UniRef with stratification. Both tools process paired-end or single concatenated FASTQ from environmental, sewage, or clinical surveillance studies, producing comprehensive community analysis.
Ensure metagenomics profiling reproducibility by exporting a reproducibility bundle containing commands.sh, environment.yml, and checksums.sha256. The pipeline automatically generates publication-quality figures and these bundles so researchers and public-health teams can validate shotgun metagenomic sequencing analysis.
Demo precomputed datasets are available for rapid testing of the shotgun metagenomics pipeline. Researchers can run the profiler on these datasets to validate Kraken2 classification, Bracken re-estimation, and RGI CARD resistome detection workflows before applying them to environmental or clinical surveillance FASTQ files.
HUMAnN3 functional pathway profiling is optional in this metagenomics pipeline. If your research focuses solely on species-level taxonomy or antimicrobial resistance gene detection rather than MetaCyc pathway abundances, you can skip HUMAnN3 and rely on Kraken2, Bracken, and RGI outputs.
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