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bcl2fastq - Illumina BCL to FASTQ conversion utility

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Illumina provides bcl2fastq and bcl2fastq2 for conversion of raw BCL (base call) files to FASTQ format.  Certain versions of the software are appropriate for corresponding models of the Illumina sequencer generating the BCL files.  Here we loosely refer to bcl2fastq to cover all the versions, although only bcl2fastq2 has been installed on Breezy as of this writing (2015-11-30).

Restrictions / License Information

Illumina provides the software for research purposes only.  It is not for use in diagnostic procedures.

Running bcl2fastq on Breezy

Version of bcl2fastq has been installed on Breezy in /global/software/bcl2fastq/bcl2fastq216. The user guide indicates that this is for use with MiSeq, HiSeq, NextSeq 500 and HiSeq X Systems.  Type

/global/software/bcl2fastq/bcl2fastq216/bin/bcl2fastq -v


/global/software/bcl2fastq/bcl2fastq216/bin/bcl2fastq -h

for information about the default options for the program and command line arguments.  In particular, note the options for controlling the number of threads used by different parts of the program.  In particular, make sure that the -p option is specified as $PBS_NUM_PPN, so that it doesn't try to use more threads for the main processing step than assigned to the job by the batch system:

/global/software/bcl2fastq/bcl2fastq216/bin/bcl2fastq -p $PBS_NUM_PPN <other options>


2015-11-30 - Created page.

System Breezy
Version 2.16