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README.md

MultiReport for Quartet DNA-Seq

MultiReport is a plugin based on MultiQC, providing additional tools which are specific to DNA-Seq quality control of Quartet Project.

For more information about Quartet Project, see http://chinese-quartet.org/

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

Usage

To use this plugin, you need to install MultiQC and install quartet-dnaseq-report.

# Install MultiQC
pip install multiqc

# Install quartet-dnaseq-report
git clone https://github.com/chinese-quartet/quartet-dseqc-report.git
cd quartet-dnaseq-report
python setup.py install

The input files for the MultiReport is the output result of Quartet DNA-Seq pipeline:

  • call-fastqc
  • call-fastqscreen
  • call-qualimap
  • call-extract_tables
  • call-merge_mendelian

Then, you can get the QC report by the following actions:

# E.g., save all data into the folder `results`
multiqc ./results/

# For the results which is not belong to Quartet DNA-Seq pipeline, you can use the the original MultiQC
multiqc ./results/ --disable-plugin

When you run the plugin, please in the quartet-dnaseq-report directory.

Development

If you're developing this code, you'll want to clone it locally and install it manually instead of using pip:

git clone https://github.com/chinese-quartet/quartet-dseqc-report.git
cd quartet-dnaseq-report/report
# You don't need to rerun the installation every time you make an edit (though you still do if you change anything in setup.py).
python setup.py develop