#get help
fastqc --help
#run on a single file
fastqc myfile.fastq.gz -o outputfolder --threads 1
#run on multiple files (assumes that the fastq files are in a folder called my_reads)
fastqc my_reads/*gz -o outputfolder --threads 20FastQC
Introduction
FastQC is a quality control tool for high throughput sequence data. For help with interpreting the output, please visit the website with some very good examples.
FastQC can be run both on short- and long-read data.
Available on Crunchomics: Yes
Installation
FastQC already is installed on Crunchomics, if you want to install it on your own system check out the instructions found here.
Usage
- Inputs: FastQC can process bam,sam,bam_mapped,sam_mapped and fastq files
- Output: An HTML quality report
Example code: