alterlab-qiime2-amplicon

name	alterlab-qiime2-amplicon
description	Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux quality .qzv), feature-classifier classify-sklearn against a version-matched SILVA 138 or Greengenes2 classifier, and diversity core-metrics-phylogenetic — teaching the .qza/.qzv artifact-and-provenance model and the 2026.1 feature-table summarize change (the former summarize_plus). Use when the request mentions QIIME2, QIIME 2, qiime, 16S, 18S, ITS, amplicon, microbiome, ASV, DADA2 denoising, feature table, taxonomic classification, or core-metrics diversity. For downstream alpha/beta diversity, PCoA, and PERMANOVA on the exported feature table prefer alterlab-scikit-bio; this is conda-only (no pip install). Part of the AlterLab Academic Skills suite.
license	MIT
allowed-tools	Read Write Edit Bash(python:*) Bash(uv:*) Bash(qiime:*) Bash(conda:*)
compatibility	Requires the QIIME 2 amplicon conda environment (cannot be pip-installed); commands are run via the `qiime` CLI. Pretrained classifiers and reference data are downloaded from the QIIME 2 Library. The helper scripts in scripts/ are stdlib-only and run under `uv run python` without a QIIME 2 env.
metadata	{"skill-author":"AlterLab","version":"1.0.0"}

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:

• "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 Trigger — route these elsewhere

The request is really about…	Route to
Alpha/beta diversity, UniFrac, PCoA ordination, PERMANOVA on an already-exported feature/distance table (in-memory, Python)	alterlab-scikit-bio
Building / manipulating a phylogenetic tree, tree visualization, or comparative phylogenetics outside QIIME 2	alterlab-phylogenetics / alterlab-etetoolkit
Shotgun metagenomics taxonomic profiling, MAG assembly, functional genes (not marker-gene amplicons)	not in this skill — amplicon only; flag the gap
RNA-seq transcript quantification (salmon/kallisto), differential expression	alterlab-rnaseq-quant → alterlab-pydeseq2
Variant calling FASTQ → VCF (germline/somatic)	alterlab-nf-core-sarek