Using MultiQC

Overview

• MultiQC is a tool for aggregating NGS QC reports.
  
  • It does not produce reports, just combines them for unified visualization.
• MultiQC "knows" the report formats of many existing NGS tools: 
  • FastQC, cutadapt, bowtie2, tophat, STAR, kallisto, HISAT2, samtools, featureCounts, HTSeq, MACS2, Picard, GATK
  • … and more!
• MultiQC can also be configured to display other data via two straightforward steps:

1. format the data appropriately (e.g. tab-delimited text files)
2. create appropriate custom data entries in a multiqc_config.yaml configuration file

• MultiQC produces neat, interactive plots in an HTML file.
  
  • So it can be used as a basic plotting tool for many kinds of reports and data, not just those produced by NGS tools!

References

Main MultiQC links

• Website: http://multiqc.info/
• Documentation: http://multiqc.info/docs
• MultiQC Github repo: https://github.com/ewels/MultiQC
• MultiQC test data repo: https://github.com/ewels/MultiQC_TestData

MultiQC configuration files

• an example multiqc_config.yaml file: https://github.com/ewels/MultiQC/blob/master/multiqc_config_example.yaml
• all multiqc_config.yaml defaults: https://github.com/ewels/MultiQC/blob/master/multiqc/utils/config_defaults.yaml

MultiQC custom data support

• structure of the custom data area of multiqc_config.yaml:
  • http://multiqc.info/docs/#configuration
• available plot types:
  
  • http://multiqc.info/docs/#plotting-functions
  • while this section is written for Python programming, the options listed in each plot type's "config" block can be specified declaratively in any plot's pconfig section in the multiqc_config.yaml.
• example custom data files from their test data repo:
  • https://github.com/ewels/MultiQC_TestData/tree/master/data/custom_content/no_config
  • https://github.com/ewels/MultiQC_TestData/tree/master/data/custom_content/embedded_config