Installation

Installation

1. Install conda/mamba. See https://docs.conda.io/en/latest/miniconda.html for miniconda installation instructions; mamba speeds up environment creation and package installation.

2. Install QIIME2. See https://library.qiime2.org for current instructions — QIIME2's amplicon distribution is now named rachis-qiime2 (renamed from qiime2-amplicon, from the 2026.4 release onward). For example, for the current release:

   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

3. Activate the environment and install ITSxpress (this also registers the qiime itsxpress plugin used by this pipeline) and BBTools/BBMap (provides bbduk.sh, used for --min-len/--max-len read-length filtering and by validation/run_validation.sh -- see Validation suite). Neither is installed by the QIIME2 environment file itself, so both are worth installing upfront rather than hitting a missing-tool error later:

   conda activate rachis-qiime2-2026.7   # name may differ depending on when you installed it
   conda install -c bioconda -c conda-forge itsxpress bbmap
   qiime dev refresh-cache                # picks up the newly installed itsxpress plugin
   
   pip install qiime2-its                 # from PyPI: https://pypi.org/project/qiime2-its/
   
   # Test the pipeline:
   qiime2-its -h

   pip install qiime2-its must run inside the activated QIIME2 environment: the package drives that environment's qiime command and checks for it at start-up. To upgrade later, pip install -U qiime2-its in the same environment. To work from a clone instead (for the validation suite, or to contribute), see Development.

Next: build a classifier, then see Pipeline usage.