QIIME2_ITS

QIIME2 pipeline for single-end (IonTorrent) and paired-end (Illumina) ITS metabarcoding data. ITSxpress for ITS region extraction, DADA2 for denoising, plus diversity statistics, classification, and a PDF summary report.

Quick start

# 1. Install QIIME2 (see the wiki for details/troubleshooting):
VERSION=2026.7  # check https://library.qiime2.org/quickstart/qiime2 for the current release
conda env create -n rachis-qiime2-$VERSION \
    --file https://raw.githubusercontent.com/qiime2/distributions/dev/$VERSION/qiime2/released/rachis-qiime2-linux-64-conda.yml
conda activate rachis-qiime2-$VERSION

# 2. Install ITSxpress + BBMap into it, and this package:
conda install -c bioconda -c conda-forge itsxpress bbmap
qiime dev refresh-cache

git clone https://github.com/duceppemo/QIIME2_ITS
cd QIIME2_ITS
pip install -e .

# 3. Run it:
qiime2-its \
    -q rachis-qiime2-$VERSION \
    -i /input_folder/ -o /output_folder/ \
    -m qiime2_metadata.tsv -c classifier.qza \
    -pe --extract-its2 --taxa Fungi

That's the short version. See the wiki for: full installation, building a classifier (UNITE/NCBI/your own fasta), the complete flag reference, fastq/metadata requirements, the diversity-stats-and-PDF-report feature, the real-data validation suite, and troubleshooting.

License

MIT