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QIIME2_ITS wiki

QIIME2 pipeline for single-end (IonTorrent) and paired-end (Illumina) ITS metabarcoding data. Uses the qiime itsxpress plugin to extract the ITS1/ITS2 region and DADA2 for denoising, then runs phylogeny, diversity, taxonomic classification, and (by default) diversity/composition/classifier statistics and a PDF summary report.

The README covers a quick install and a minimal run. Everything else lives here:

• Installation — full QIIME2 + ITSxpress + BBMap setup
• Building a classifier — UNITE, NCBI, or your own fasta file
• Pipeline usage — the full qiime2-its flag reference
• Metadata and fastq naming requirements — the Casava naming scheme, common gotchas
• Advanced stats and the PDF report — group-significance tests, genus-level composition, sample classification, report.pdf
• Worked example — a real 53-sample public dataset from SRA accession to PDF report: every script, the metadata, and the report itself to look at before you try it
• Validation suite — the real-data validation suite and its audit trail
• Development — running the unit tests, project layout
• Troubleshooting / FAQ

Issues and pull requests: https://github.com/duceppemo/QIIME2_ITS