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.
See it before you try it: a complete example report (PDF) from a real 53-sample public SRA dataset, with every script needed to reproduce it -- worked example.
# 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-$VERSION
# 2. Install ITSxpress + BBMap into it, and this package:
conda install -c bioconda -c conda-forge itsxpress bbmap
qiime dev refresh-cache
pip install qiime2-its
# 3. Run it:
qiime2-its \
-q rachis-qiime2-$VERSION \
-i /input_folder/ -o /output_folder/ \
-m qiime2_metadata.tsv -c classifier.qza \
-pe --extract-its2 --taxa FungiThat'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, a worked example on public SRA data, the real-data validation suite, and troubleshooting.