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from Bioclaw Skills Hub23
Complete shotgun metagenomics workflow including host-depletion QC, taxonomic profiling, functional analysis, and AMR summaries.
This skill provides a standardized pipeline for analyzing shotgun metagenomic data. It guides the agent through the entire process from raw FASTQ files to reproducible community output tables, ensuring high-quality genomic insights.
Use this skill when processing shotgun metagenomics data (as opposed to amplicon sequencing) to determine species or genus abundances, functional pathway profiles, or antimicrobial resistance (AMR) summaries across multiple samples.
Designed for agents with shell execution capabilities such as Claude Code, Cursor, or OpenClaw.
This skill has not been reviewed by our automated audit pipeline yet.
Seq Wrangler
Sequence data QC, trimming, alignment, and BAM processing pipeline helper — wraps FastQC, fastp/Trimmomatic, BWA/Bowtie2/Minimap2, and SAMtools for automated re
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