## Quality control / 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]

### 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.

### 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".

### Reference

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