Bcl2fastq2

bcl2fastq version 2.20.0 is used to convert bcl files to FASTQ, and is compatible with MiniSeq, MiSeq, NextSeq 500, all HiSeq (2000, 2500, 3000, 4000, and HiSeqX), and NovaSeq 5000/6000systems running RTA version 1.18.54 and above [1].

Module

List the versions available as modules:

module spider bcl2fastq2

Output:

--------------------------

  bcl2fastq2: bcl2fastq2/2.20.0

--------------------------

...

See how to load the version you need:

module spider bcl2fastq2/<version>

Load any required modules that are reported by the spider command, and then load the bcl2fastq2 module:

module load bcl2fastq2/<version>

Usage

The bcl2fastq command will print usage information when the --help flag is specified:

bcl2fastq --help

References