alterlab-qiime2-amplicon

# 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: - "Run a QIIME 2 16S pipeline on my paired-end reads." - "I have ITS amplicon FASTQs — denoise with DADA2 and assign taxonomy." - "Build a feature table / ASV table and classify against SILVA." - "Pick truncation lengths from my quality plot and run core-metrics diversity." - "How do I trim primers before DADA2 in QIIME 2?" - "What's the right order of QIIME 2 commands?" ### Does NOT Trigge...