Metadata-Version: 2.4
Name: multiqc_sav
Version: 0.1.0
Summary: MultiQC plugin for Illumina SAV InterOp visualizations
Author-email: Matthias De Smet <matthias.desmet@ugent.be>
License: MIT
Project-URL: Homepage, https://github.com/MultiQC/MultiQC_SAV
Project-URL: Repository, https://github.com/MultiQC/MultiQC_SAV
Project-URL: Issues, https://github.com/MultiQC/MultiQC_SAV/issues
Keywords: bioinformatics,illumina,sequencing,multiqc
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
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
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: multiqc>=1.25
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: interop<2,>=1.7.0
Provides-Extra: dev
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Dynamic: license-file

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![Build status](https://github.com/MultiQC/MultiQC_SAV/actions/workflows/linux.yaml/badge.svg)
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/multiqc_sav/README.html)
[![Anaconda-Server Badge](https://anaconda.org/bioconda/multiqc_sav/badges/downloads.svg)](https://anaconda.org/bioconda/multiqc_sav)
[![Anaconda-Server Badge](https://anaconda.org/bioconda/multiqc_sav/badges/latest_release_date.svg)](https://anaconda.org/bioconda/multiqc_sav)
[![Anaconda-Server Badge](https://anaconda.org/bioconda/multiqc_sav/badges/version.svg)](https://anaconda.org/bioconda/multiqc_sav)

**MultiQC_SAV is a plugin for MultiQC, leveraging the [InterOp python API](https://github.com/Illumina/interop) to generate the most used tables and graphs from the Illumina SAV**

For more information about MultiQC, see [http://multiqc.info](http://multiqc.info)

For more information about Illumina SAV, see [the Illumina support page](https://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav/downloads.html)

## Description

The MultiQC_SAV plugin parses the InterOp files in an Illumina Sequencer output directory and generates tables and graphs of the most important metrics

## Example

An example report can be found [here](docs/example/NextSeq500_report.html)

## Installation

This plugin can be installed using the following methods

- using `pip`:

```bash
pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC_SAV.git
```

- using `conda`:

```bash
conda install -c bioconda multiqc_sav
```

- using `setuptools`:

```bash
git clone https://github.com/MultiQC/MultiQC_SAV
cd MultiQC_SAV
python setup.py install
```

## Usage

This plugin adds a QC module and searches for the `RunInfo.xml` and `RunParameters.xml` files. It tries to infer if all required files are present. No special params are needed.

### Required files

The illumina directory should contain the following files the directory structure as dictated by the sequencer

```bash
illumina_dir
├── InterOp
│   ├── *.bin
├── RunInfo.xml
├── RunParameters.xml

```

### Contributors

- Matthias De Smet [@matthdsm](https://github.com/matthdsm), [@CenterForMedicalGeneticsGhent](https://github.com/CenterForMedicalGeneticsGhent)
