Read quality with FastQC

Description

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

Parameters

File type (bam, fastq) [fastq]
Create input for MultiQC (yes, no) [no]

Details

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:

Set the parameter Create input for MultiQC = yes. This will produce an mqc file. You can then select the mqc files for samples and run the tool Quality control / Combine reports using MultiQC
Make a tar package of all the FASTQ files using the tool Utilities / Make a tar package and run the tool Quality control / Read quality with MultiQC for many FASTQ files.

Output

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.

Reference

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