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bgzipped ref fasta take much longer time #260

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baozg opened this issue Nov 12, 2024 · 1 comment
Open

bgzipped ref fasta take much longer time #260

baozg opened this issue Nov 12, 2024 · 1 comment
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performance Issues related to computational perfromance third-party problem Problem is related to other tools, libraries, system etc

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@baozg
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baozg commented Nov 12, 2024

Hi,

Didi IsoQuant support bgzipped reference fasta? I have a chance to run same bam with / without bgzipped fasta. The uncompressed fasta run took ~1h to finish, but the compressed run more than 24 hours

@andrewprzh
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@baozg

I think I never tested performance on bzgipped reference. It seems that the library I use (pyfaidx) is not very efficient in this case (and IsoQuant does use reference genome a lot). Although it supposed to make an index.

I will test it and see what can be done, at least a warning can be useful - thanks for the report!

Best
Andrey

@andrewprzh andrewprzh added performance Issues related to computational perfromance third-party problem Problem is related to other tools, libraries, system etc labels Nov 18, 2024
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