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qiime2-workflow

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Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (FeatureTable[Frequency], SampleData[PairedEndSequencesWithQuality], Phylogeny[Rooted], FeatureData[Taxonomy]), embedded provenance plus provenance replay, import (Casava/manifest/EMP/BIOM), export, the Metadata object, and the q2cli vs Artifact API interfaces. Covers why a .qza is data-plus-executable-history not a file, why export drops provenance, why a .qzv is terminal, why classifier .qza are version-pinned, and the 2026 distribution/rachis rename. Use when importing reads, choosing a manifest/Casava/EMP/BIOM path, reading or replaying provenance, exporting to BIOM/phyloseq, fixing semantic-type or Phred or sklearn-version errors, or orchestrating the pipeline. Denoising -> amplicon-processing; classifier/DB -> taxonomy-assignment; diversity metric/depth -> diversity-analysis; DA tool -> differential-abundance; PICRUSt2 -> functional-prediction; shotgun moshpit -> met…

When to use

• importing reads
• choosing a manifest/Casava/EMP/BIOM path
• reading or replaying provenance
• exporting to BIOM/phyloseq
• fixing semantic-type or Phred or sklearn-version errors
• orchestrating the pipeline
• managing .qza/.qzv artifacts
• using q2cli vs Artifact API interfaces

When not to use

• denoising
• classifier/DB choice + training
• diversity metric/sampling-depth/rarefaction
• DA tool choice/consensus
• PICRUSt2
• shotgun moshpit
• metagenomics
• re-teaching the method

Skill page

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