bcl2fastq

Conversion software that demultiplexes sequencing data and converts base call (BCL) files into FASTQ files

Homepage Version(s): 2.20.0

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bcl2fastq requires an environment module

In order to use bcl2fastq, you must first load the appropriate environment module:

module load gnu bcl2fastq

The bcl2fastq program is a data converter for bioinformatics data produced by Illumina sequencers. It is able to convert BCL formatted sequence data to FASTQ sequence data.

Using bcl2fastq on the HPC

# Load environment modules
$ module load gnu bcl2fastq

# Execute the command  
$ bcl2fastq -OPTIONS FILES

Detailed information on usage and command line options can be found either by running bcl2fastq --help to see a list of command line options or by referring to the User's Guide.