Bcl2fastq2
Description
The Illumina sequencing instruments generate per-cycle base call (BCL) files at the end of the sequencing run. A majority of analysis applications use per-read FASTQ files as input for analysis. You can use the bcl2fastq2 Conversion Software to convert basecall (BCL) files from a sequencing run into FASTQ files.
The bcl2fastq2 Conversion Software supports the following instruments:
- MiniSeq
- MiSeq
- NextSeq 500, 550
- HiSeq X
- HiSeq 2000, 2500, 3000, 4000
License
This Software is licensed for use under an End User Software License Agreement
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of obcl2fastq2 and load default version of obcl2fastq2 as
module avail obcl2fastq2/ # list available modules module load obcl2fastq2 # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail obcl2fastq2
and choose explicit version you want to use.
Documentation
Homepage
https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html