/qiime2-amplicon

name: qiime2-amplicon
description: Processes paired-end 16S amplicon reads into QIIME 2 ASVs and taxonomy with retained artifact provenance. Checks paired FASTQ manifests, primer orientation diagnostics, predicted post-trimming overlap, sample IDs, runtime versions and read retention, and guides selection of compatible taxonomic classifiers.
license: MIT
compatibility: Python 3.10+ for the standard-library validation helper; QIIME 2 2026.7 distribution with cutadapt, dada2, demux, feature-table, feature-classifier, taxa and types plugins for execution. Install through the official conda/container distribution, not PyPI. Requires a compatible trusted classifier and network for installation/reference downloads.
metadata:
  version: "1.1"
  skill-author: K-Dense Inc.
  upstream-version: "2026.7"
  last-reviewed: "2026-10-01"

QIIME 2 paired-end 16S amplicons

Use for a demultiplexed, paired-end 16S assay with known primers, quality encoding, expected insert length, and sample metadata. This bounded workflow imports reads, removes 5′ primers, denoises with DADA2, classifies ASVs using an explicitly supplied classifier, and retains `.qza`/`.qzv` provenance. Do not treat read counts as absolute cell counts or taxonomy assignments as strain identification.

Establish the assay before running

• Confirm Phred+33, read orientation, primer sequences **as sequenced** in forward/reverse reads,

and whether primers have already been removed. The bundled runner requires primers still present at the 5′ ends; it anchors Cutadapt matching and discards untrimmed pairs. Already trimmed reads need a direct import → DADA2 workflow with that omission recorded in provenance.

• Choose truncation positions from actual per-base quality and error profiles. `trunc-f/r` are

positions **after primer removal**. The expected maximum insert length also excludes primers. Require `trunc_f + trunc_r - maximum_insert_length >= 12`; use a margin for length variation. The check predicts geometrical overlap, not successful biological merging.

• Choose a classifier whose reference database, taxonomic coverage, orientation and training

approach fit the assay. Full-length classifiers are supported; primer-region-specific training is not mandatory. Match its scikit-learn version exactly to the installed environment (the official 2026.7 distribution pins 1.7.1). Record source URL, database version and checksum. QIIME's current data-resources page links externally hosted classifiers for 2026.4 and later; its older downloads are not automatically compatible. Do not automatically fetch an arbitrary “latest” classifier or reuse an incompatible serialized sklearn model. Load sklearn classifier artifacts only from trusted sources: QZA format validation does not make an untrusted serialized model safe.

• Include extraction blanks, PCR negatives, and a mock community where available. The runner

rejects empty FASTQs; preserve empty-control IDs separately and report them rather than silently deleting control evidence. Assess contamination before ecological interpretation.

Input files

Manifest is a **tab-separated** `PairedEndFastqManifestPhred33V2` file with exactly these headers:

sample-id	forward-absolute-filepath	reverse-absolute-filepath
sample1	/data/sample1_R1.fastq.gz	/data/sample1_R2.fastq.gz

This is the helper's deliberately narrow manifest profile. Use actual tab characters, literal absolute paths visible to the runtime (expand environment variables before calling this helper), and one row per sample; no comment/directive rows or additional columns in this manifest. Do not reverse-complement R2 files. Sample metadata is a tab-separated file with first column `sample-id`, unique IDs matching the manifest, and optional `#q2:types` annotation. Include covariates and biological replicate IDs needed downstream. The helper checks metadata IDs and row structure; QIIME performs full metadata typing/directive validation during execution. Metadata used by actions persists in artifact provenance, so use de-identified biological replicate IDs.

Execute

The helper lives at [scripts/amplicon_workflow.py](scripts/amplicon_workflow.py). Commands below assume the skill directory is the working directory. First validate without QIIME. These example primers and lengths are **illustrative**, not universal assay settings:

python scripts/amplicon_workflow.py validate \
  --manifest manifest.tsv --metadata sample-metadata.tsv \
  --primer-f GTGYCAGCMGCCGCGGTAA --primer-r GGACTACNVGGGTWTCTAAT \
  --trunc-f 220 --trunc-r 200 --amplicon-max 300

Then run in the QIIME 2 2026.7 environment with a compatible classifier. This study-specific invocation is illustrative; choose lengths using a preceding quality inspection or pilot:

python scripts/amplicon_workflow.py run \
  --manifest manifest.tsv --metadata sample-metadata.tsv \
  --primer-f GTGYCAGCMGCCGCGGTAA --primer-r GGACTACNVGGGTWTCTAAT \
  --trunc-f 220 --trunc-r 200 --amplicon-max 300 \
  --classifier compatible-classifier.qza --threads 4 --output run01

`run` executes immediately, writes only to a fresh output directory, and stops on a failing QIIME command. It streams through every paired FASTQ record to catch mismatched IDs/order/counts, checks sequence/quality consistency and sample alignment, and profiles the first 1,000 read pairs for exact IUPAC primer matches. Low exact-match rates are warnings: Cutadapt allows mismatches, but a low rate can also indicate incorrect orientation, adapters, or already-trimmed data. At least one complete pair per sample must meet nominal post-primer truncation lengths. These length estimates subtract the stated primer lengths; they do not simulate Cutadapt indels or quality filtering, and do not establish that any pair will actually merge.

The runner uses `--output-dir` for plugin methods with evolving output sets, preserving Cutadapt statistics and DADA2 base-transition art