What problem does it solve?
Marker-gene microbiome studies require coordinating primer trimming, ASV inference, taxonomy assignment, and diversity analysis across multiple bioinformatics tools, and misconfigured primers or taxonomy databases silently invalidate results. This Skill structures that workflow so amplicon FASTQs become auditable ASV tables, taxonomy assignments, and diversity metrics.
Core Features & Use Cases
- Read QC and Readiness Packaging: Validates sample sheets, runs seqkit stats and FastQC/MultiQC, and emits machine-readable QC verdicts and visualization dashboards before any backend run.
- Multi-Backend ASV and Taxonomy Execution: Runs QIIME2, DADA2 (via Rscript), or nf-core/ampliseq with explicit primer sequences, truncation choices, and taxonomy classifiers, producing normalized ASV tables, representative sequences, and read-retention reports.
- Diversity and Visualization Outputs: Generates alpha diversity, Bray-Curtis distances, PCoA, rarefaction, and taxa barplots when feature tables exist, and blocks unsupported claims when they do not.
- Use Case: A researcher with paired-end 16S V4 FASTQs provides primer sequences, a SILVA 138 classifier, and sample metadata; the Skill runs the QIIME2 backend and delivers ASV, taxonomy, and diversity tables plus an HTML dashboard.
Quick Start
Ask the assistant to inspect your amplicon FASTQ sample sheet, confirm primer sequences and taxonomy database, and run the amplicon microbiome preflight and backend analysis.
