Metadata-Version: 2.4
Name: qiime2-its
Version: 0.3.2
Summary: QIIME2 ITS metabarcoding pipeline for single-end (IonTorrent) and paired-end (Illumina) data
Author: duceppemo
License-Expression: MIT
Project-URL: Homepage, https://github.com/duceppemo/QIIME2_ITS
Project-URL: Repository, https://github.com/duceppemo/QIIME2_ITS
Project-URL: Documentation, https://github.com/duceppemo/QIIME2_ITS/wiki
Project-URL: Issues, https://github.com/duceppemo/QIIME2_ITS/issues
Project-URL: Changelog, https://github.com/duceppemo/QIIME2_ITS/releases
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.81
Requires-Dist: matplotlib>=3.7
Requires-Dist: pandas>=2.0
Requires-Dist: fpdf2>=2.7
Requires-Dist: scipy>=1.10
Provides-Extra: dev
Requires-Dist: pytest>=7.4; extra == "dev"
Requires-Dist: pytest-mock>=3.12; extra == "dev"
Requires-Dist: pytest-cov>=4.1; extra == "dev"
Dynamic: license-file

<p align="center">
  <img src="https://raw.githubusercontent.com/duceppemo/QIIME2_ITS/master/docs/QIIME2_ITS_logo.png" alt="QIIME2_ITS logo" width="280">
</p>

<h1 align="center">QIIME2_ITS</h1>

<p align="center">
  <a href="https://github.com/duceppemo/QIIME2_ITS/actions/workflows/tests.yml"><img src="https://github.com/duceppemo/QIIME2_ITS/actions/workflows/tests.yml/badge.svg" alt="tests"></a>
  <a href="https://github.com/duceppemo/QIIME2_ITS/blob/master/LICENSE"><img src="https://img.shields.io/github/license/duceppemo/QIIME2_ITS" alt="license"></a>
  <img src="https://img.shields.io/badge/python-3.9%2B-blue" alt="python 3.9+">
  <img src="https://img.shields.io/badge/QIIME2-2026.x-blue" alt="QIIME2 2026.x">
</p>

<p align="center">
  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.
</p>

## Quick start

```bash
# 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](https://github.com/duceppemo/QIIME2_ITS/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](https://github.com/duceppemo/QIIME2_ITS/blob/master/LICENSE)
