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mgikit-multiqc Plugin

General Information

mgikit plugin is a plugin incorporated with the MultiQC tool in order to read the logs and reports generated by the MGIKIT demultiplexer and generate a quality control report similar to what a user gets when using bcl2fastq tool. If you have any questions, please get in touch on Github

Installation

To use this plugin, you need to have MultiQC installed and then install this plugin. For example:

pip install MultiQC
git clone https://github.com/sagc-bioinformatics/mgikit-multiqc
cd mgikit-multiqc
python setup.py install

# To test the installation, run the following
multiqc MGIKIT-examples/test/

Input files

This plugin reads the log files of MGIKIT demultiplexing tool. The possible output files are:

1. General info file ('*.L{1,2,3,4}.mgikit.general'): This file contains information related to the reads generated by a specific lane including quality scores, cluster count...
2. General info file ('*.L{1,2,3,4}.mgikit.info'): This file contains information about the matching indexes within the data generated by a specific lane.
3. Undetermined barcodes file ('*.L{1,2,3,4}.mgikit.undetermined_barcode'): This file contains the information about the barcodes that did not match with any sample.
4. Ambiguous barcodes file ('*.L{1,2,3,4}.mgikit.ambiguous_barcode'): This file contains the information about the barcodes that match with multiple samples. This situation can happen when setting a high mismatch threshold.

Parameters

All parameters below are optional:

• --disable-mgikit-plugin: Disable the mgikit MultiQC plugin on this run. The default is False.
• --undetermined-barcode: The number of undetermined barcodes to be presented in the report. It takes any positive value less than or equal to the number of barcodes in the demultiplexer reports which is usually 50. The default is 25.
• --decimal-positions: The number of decimal positions to be used with the values in the tables of the mgikit plugin. 2 decimal positions are the default option.
• --brief-report: Generate a brief version of the report. This ignores the reports for cluster per sample per lane. The default is False.
• --keep-core-samples: Ignore undetermined and ambiguous cases in the report. The default is False.

Usage

When running MultiQC (after installing the mgikit plugin), the plugin will check for the mgikit reports and logs and find the relevant one based on the suffix of the file names. When reports are detected, the plugin will generate the relevant QC and attach them to the main MultiQC report under the MGIKIT section.

For example:

multiqc mgikit-examples/test/