domains / families / science / qiime2-amplicon

qiime2-amplicon

separate

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.

When to use

• demultiplexed, paired-end 16S assay
• known primers, quality encoding, expected insert length
• sample metadata
• imports reads
• removes 5′ primers
• denoises with DADA2
• classifies ASVs using an explicitly supplied classifier
• retains .qza/.qzv provenance

When not to use

• treat read counts as absolute cell counts
• taxonomy assignments as strain identification

Skill page

Source