| name | ngs-shotgun-metagenomics |
| description | Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN. |
Shotgun Metagenomics
Use this skill for shotgun metagenomic FASTQs.
Essential Inputs
Confirm:
- paired-end or single-end reads
- host organism and host-depletion requirement
- target outputs: taxonomic profile, functional profile, assembly, binning, or QC only
- preferred database family, if any
- database paths or permission to download large databases
- sample metadata, batches, and negative controls
Public Defaults
Prefer nf-core/taxprofiler for reproducible taxonomic profiling. Use direct Kraken2/Bracken, MetaPhlAn, or HUMAnN when the user wants a focused path or already has databases installed.
For direct backend execution, prefer the plugin runner over handwritten shell when possible because it validates database bundle contents and records resources/resource_plan.json, resource_manifest.tsv, resource_env.sh, and resource_readiness.md. --run-bracken and --run-humann make those database bundles blocking, not merely optional.
Preflight
python plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline shotgun_metagenomics --emit-install-plan
Local Execution Package
For FASTQ intake/QC before host-depletion, taxonomic profiling, or functional profiling, use:
python plugins/ngs-analysis/scripts/run_fastq_assay_package.py \
--lane shotgun_metagenomics \
--sample-sheet shotgun_samples.csv \
--execute
This validates read paths and structure, runs seqkit stats and FastQC/MultiQC when available, and writes . Add only when a local Kraken2 database is available; otherwise the package records the database/tool blocker explicitly.
