Does Illumina's bcl2fastq command line tool have a way to pipe to stdout immediately
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3.3 years ago
b10hazard • 0

Does Illumina's bcl2fastq command line utility have a way to pipe the base calls immediately to stdout? Right now I have to wait the 1 hour or so it takes for bcl2fastq to make a gzip file that I can unzip. I'd like to immediately pipe this data to stdout if possible. I don't see a command line option in the documentation to do this. If this is not possible; is there any application that will immediately pipe these calls to stdout?

bcl2fastq illumina next-gen • 690 views
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I don't think so. If you just want no compression on the files then run bcl2fastq with the following option.

--no-bgzf-compression                           turn off BGZF compression for FASTQ files

You would still not be able to use the files until the run is done.

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