MultiQC

Goal

Generate an overview report for all illumina findings

Background

Consulting all reports individually for each read file and each software tool ca be a laborious task. Luckily, there exists solutions for aggreagating such information into a simple yet intuitive report. One option is to use MultiQC, a programm which attempts to autodetect existing report files from the directory you specify, and then swiftly generate a single html report for easy inspection and sharing.

Practical

In this exercise you will learn to inspect MultiQC documentation in order to set up your analysis to provide the output files and/or applying file naming conventions for enabling MultiQC to detect and implement results from different tools (hence referred as Modules).

Instructions

We assume you have MultiQC preinstalled.

  1. Since MultiQC utilizes output from many different software tools as modules, inspecting the documentation is crucial for setting up you analysis to provide the files you need. Go to the following site and inspect which supported modules are relevant for the course:
Supported Tools - MultiQC
MultiQC currently has modules to support 132 different bioinformatics tools, listed below.
https://multiqc.info/modules/

Note: Currently (as of version 1.15) NanoPlot is yet to be supported in the stable release of MuliQC. However on the official Github page (https://github.com/ewels/MultiQC), there are fixes that should enable import of NanoPlot files, they are just only released on the development version.

  1. Lets start out by inspecting its help page
multiqc --help
  1. Now it should be quite apparent that some work needs to be put into the output of the different tools. If you used the full command in the trimmomatic exercise, you should have created a Ec003_trim_out.log file. Navigate to the illumina folder, and make sure that you have the fastqc files and trimmomatic file somewhere within the folder (e.g. in a fastqc_reports/ and trimmomatic/ directory) and execute MultiQC
multiqc .

Note: . refers to current directory

That’s it!!

đź’ˇ
Utilise the --outdir (-o) to specify which directory output files should be written to. If your files doesn’t get detected, try running with --verbose to get more details. Remember to check out the supported tools page on the specific module for help. Alternately inspect the source code on the individual modules on Github, as there might be some hints to gather from there.
https://github.com/ewels/MultiQC/tree/master/multiqc/modules