https://github.com/multiqc/multiqc_sav

MultiQC plugin replicating the most used plots and tables from Illumina's SAV
https://github.com/multiqc/multiqc_sav

Last synced: 12 months ago
JSON representation

MultiQC plugin replicating the most used plots and tables from Illumina's SAV

• Host: GitHub
• URL: https://github.com/multiqc/multiqc_sav
• Owner: MultiQC
• License: mit
• Created: 2021-06-01T08:42:31.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2022-04-04T13:49:19.000Z (about 4 years ago)
• Last Synced: 2025-04-08T16:38:07.791Z (about 1 year ago)
• Language: Python
• Size: 223 MB
• Stars: 6
• Watchers: 1
• Forks: 1
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# [](https://github.com/ewels/MultiQC)

![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)