MultiQC_SAV is a plugin for MultiQC, leveraging the InterOp python API to generate the most used tables and graphs from the Illumina SAV

For more information about MultiQC, see http://multiqc.info

For more information about Illumina SAV, see the Illumina support page

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

Installation

This plugin can be installed using the following methods

• using pip:

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

• using conda:

conda install -c bioconda multiqc_sav

• using setuptools:

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

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

Contributors

• Matthias De Smet @matthdsm, @CenterForMedicalGeneticsGhent