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!
It can also be configured to display other data via two straightforward steps:
- format the data appropriately (e.g. tab-delimited text files)
- 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:
- 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:
