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).

Pinned to QIIME 2 2026.1 (the amplicon distribution). Forward-compat note: the distribution is renamed qiime2 in 2026.4 — the env name and channel URL change, the plugin commands below do not.

When to Use This Skill

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