QIIME 2 Amplicon — 16S/ITS Microbiome Pipeline (FASTQ → Feature Table → Taxonomy → Diversity)

The command-line, workflow-runner entry point for marker-gene (amplicon) microbiome analysis. Given raw demultiplexed paired-end reads, it walks the canonical QIIME 2 order — import → primer trim → denoise → classify → diversity — and teaches the two things people get wrong most: trimming primers BEFORE DADA2, and the .qza/.qzv provenance model. It is the raw-data-to-result pipeline that hands a feature table off to in-memory analysis skills (see routing below).

Written against QIIME 2 2026.7 (released 2026-07-22), the current release. The distribution formerly called amplicon was renamed qiime2 in 2026.4, and its conda env files carry a rachis- prefix (the framework package was renamed qiime2 -> rachis in 2026.1). Only the env name, channel path, and file names moved: every plugin command below is unchanged across those releases.

When to Use This Skill

Use this skill when the request involves running an amplicon / microbiome pipeline from sequencing reads: