## Quality control / Read quality with FastQC

### Description

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

### Parameters

- Create all plots (yes, no) [no]

### Details

FastQC supports all quality encoding variants of FASTQ files. GZip compressed FASTQ files are automatically detected and unzipped. By default plots are generated for per base quality and sequence content. User can also request to get plots for GC and N content, sequence length distribution, duplication levels, overrepresented sequences and Kmer content. For a detailed description of the plots, please see the FastQC manual.

### Output

Image files (.png) for the requested plots. The plotted information is also given in text format (fastqc_data.txt).

### Reference

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