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
The MultiQC_SAV plugin parses the InterOp files in an Illumina Sequencer output directory and generates tables and graphs of the most important metrics
An example report can be found here
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 installThis 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.
The illumina directory should contain the following files the directory structure as dictated by the sequencer
illumina_dir
├── InterOp
│ ├── *.bin
├── RunInfo.xml
├── RunParameters.xml
- Matthias De Smet @matthdsm, @CenterForMedicalGeneticsGhent