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multiqc on Biowulf & Helix

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MultiQC will look through a given path and identify the log files for >20 commonly used bioinformatics tools and aggregate them into a single, stand-alone html report summarizing results for all detected samples.

The tools MultiQC knows about fall into three groups:

Pre-alignment tools
FastQC, Skewer, Cutadapt, ...
Alignment tools
Bowtie1, Bowtie2, STAR, ...
Post-alignment tools
Samtools, Samblaster, Picard, featureCounts, ...

There may be multiple versions of multiqc available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail multiqc 

To select a module use

module load multiqc/[version]

where [version] is the version of choice.

Environment variables set


On Helix

MultiQC does not require much resources and can be run either on helix or in an interactive session.

Let's copy an example RNA-seq project (only log files - no actual data) and run multiqc on it

helix$ module load multiqc
helix$ cp -r /usr/local/apps/multiqc/TEST_DATA/rna-seq .
helix$ cd rna-seq
helix$ multiqc .

This will create a directory with parsed data (multiqc_data) and a stand alone html report. The reports use templates which can be changed with --template. One template (default_dev), for example, generates graphs in multiple formats.