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

Using bcl2fastq on RCC Systems

Using this program does not required the use of any particular module. It is only available currently on our SPEAR nodes however. All that needs to be done to run this program is to login to a spear node, then run the following commands. Simply replace -OPTIONS with any command-line options appropriate to your job and FILES with the directories or filenames required for your job.

bcl2fastq -OPTIONS FILES

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

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