Amplicon Microbiome

Use this skill for marker-gene microbiome analysis from amplicon FASTQs.

Essential Inputs

Confirm:

• marker region: 16S, 18S, ITS, COI, or custom
• primer sequences and orientation
• paired-end or single-end reads
• whether reads should be merged
• taxonomy database and version
• sample metadata
• endpoint: ASV table, taxonomy, diversity, differential abundance, or plots

Public Defaults

Prefer nf-core/ampliseq for reproducible end-to-end runs. Use QIIME2 or DADA2 directly when the user wants notebook-level control or an existing lab protocol requires it.