Read quality with FastQC


Given a FASTQ or BAM file, this tool produces several quality control plots for the reads.



FastQC examines reads for base quality and distribution, duplicates, length, over-represented k-mers, etc. GZip compressed fastq files are automatically detected and unzipped. For a detailed description of the plots, please see the FastQC manual.

If you have several FASTQ files and you would like to combine their quality reports together, you have two options:


An html report with plots and tables produced by the analysis modules. Please note that you have to select the visualization option "Open in external browser".

Optionally an mqc file which you can use as input for the tool Quality control / Combine reports using MultiQC.


This tool is based on the FastQC package by Simon Andrews et al.