fastqc
Software Description
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
Info
Module Name
fastqc
Last Updated On
08/29/2023
Support Level
Primary Support
Software Access Level
Open Access
Home Page
Documentation
Software Description
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
Slurm Example
#!/bin/bash
#SBATCH --job-name="rfm_RunFASTQCTest_job"
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=rfm_RunFASTQCTest_job.out
#SBATCH --error=rfm_RunFASTQCTest_job.err
#SBATCH --time=0:10:0
#SBATCH -p small,large,ram256g,ram1t
module load fastqc/0.11.7
fastqc r1.fq r2.fq
General Linux
To load this module for use in a Linux environment, you can run the command:
module load fastqc
Depending on where you are working, there may be more than one version of fastqc available. To see which modules are available for loading you can run:
module avail fastqc
Agate Modules
Default
0.11.7
Other Modules
0.11.2, 0.11.5, 0.11.7, 0.11.8, 0.11.9
Mangi Modules
Default
0.11.7
Other Modules
0.11.2, 0.11.5, 0.11.7, 0.11.8, 0.11.9
Mesabi Modules
Default
0.11.7
Other Modules
0.11.2, 0.11.5, 0.11.7, 0.11.8, 0.11.9