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