Can I use a gpu to demultiplex with bcl2fastq?
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7.1 years ago
diltsjeri ▴ 470

Hi,

Just brainstorming ways to speed up our pipeline. Demultiplexing is definitely a time hog. I'm not too familiar with exactly how demultiplexing works computationally. Is bcl2fastq written in such a way that it could utilize our gpus? I'm not finding much documentation on the subject.

Illumina Demultiplex bcl2fastq gpu • 2.6k views
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Demultiplexing is definitely a time hog.

You will have to quantify along with information about what type of run data (sequencer, cycles etc) you are processing and on what compute infrastructure.

Otherwise I don't think it is particularly so. Latest version of bcl2fastq v.2.19 is much much faster compared to previous versions and if you have access to a cluster/high performance storage system you can process runs at a good clip using multiple threads.

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Yeah the documentation says cpus only with threading options.

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Can you contact me via email?

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7.1 years ago

No, it can't use your GPUs. Just use multithreading, it runs reasonably quickly then given how long it takes to sequence things.

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