fastq_screen

The FastQ Screen module parses results generated by FastQ Screen, a tool that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

By default, the module creates a plot that emulates the FastQ Screen output with blue and red stacked bars showing unique and multimapping read counts. This plot only works for a handful of samples however, so if # samples * # organisms >= 160, a simpler stacked barplot is shown. This is also shown when generating flat-image plots.

To always show this style of plot, add the following line to a MultiQC config file:

fastqscreen_simpleplot: true