claw-metagenomics

What problem does it solve?

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.

Core Features & Use Cases

• Taxonomic profiling: Kraken2 classification with Bracken species-level re-estimation to produce adjusted abundance tables.
• Resistome detection: RGI against CARD restricted to Perfect and Strict hits and mapped to WHO priority pathogen tiers.
• Functional profiling: Optional HUMAnN3 pathway abundance (MetaCyc/UniRef) with stratification.
• Reproducibility & Reporting: Generates publication-quality figures and a reproducibility bundle (commands.sh, environment.yml, checksums.sha256).
• Use Case: Environmental or sewage surveillance for WHO-critical ARG monitoring and comparative community analysis across sites.

Quick Start

Run the metagenomics profiler on paired-end FASTQ to produce taxonomy, resistome, pathway reports, publication figures, and a reproducibility bundle.