FastQC

A quality control application for high throughput sequence data. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Example

To obtain command line help:

/shared/opt/fastqc-0.11.9/fastqc --help

To run FastQC on the input file: galaxy_filter_by_quality_on_data_26M_solexa.fastq:

$ /shared/opt/fastqc-0.11.9/fastqc --noextract galaxy_filter_by_quality_on_data_26M_solexa.fastq 
Started analysis of galaxy_filter_by_quality_on_data_26M_solexa.fastq
Approx 5% complete for galaxy_filter_by_quality_on_data_26M_solexa.fastq
Approx 10% complete for galaxy_filter_by_quality_on_data_26M_solexa.fastq
....
Approx 95% complete for galaxy_filter_by_quality_on_data_26M_solexa.fastq
Approx 100% complete for galaxy_filter_by_quality_on_data_26M_solexa.fastq
Analysis complete for galaxy_filter_by_quality_on_data_26M_solexa.fastq
$ 

The output file will be: galaxy_filter_by_quality_on_data_26M_solexa_fastqc.zip

Installation Notes

You do not need to do this. This just documents the install on the HPC.

hpcnode01 tmp/$ 
$ wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
$ unzip fastqc_v0.11.9.zip            <== This creates directory FastQC.
$ mv FastQC fastqc-0.11.9             <== Rename directory to include version.
$ chmod 755 fastqc-v0.11.9/fastqc     <== Need to make the binary executable.
$ sudo mv fastqc-0.11.9 /shared/opt/

Check that it runs OK:

$ /shared/opt/fastqc-0.11.9/fastqc --version
FastQC v0.11.9

There is an older version which I will remove in early 2022.

$ /shared/opt/fastqc-0.10.1/fastqc --version
FastQC v0.10.1
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