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qiime2-amplicon

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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.

skills/qiime2-amplicon/SKILL.md

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# 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
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