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.