Run purge_dups with PacBio hifi reads and HiCanu assembly
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5 weeks ago
scruffener • 0

Hi there,

I was wondering if it is possible to run purge_dups on a de novo genome assembly generated with HiCanu and PacBio hifi reads without any short reads. One of the arguments in step 1 of the "usage" section in the purge_dups documentation (https://github.com/dfguan/purge_dups) requires a list of short read files. Would long reads work aswell?

Best regards, scruffener

HiCanu purge_dups hifi assembly PacBio • 236 views
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Yes, people do this routinely. The short reads are an "optional" argument.

See this example from the Canu github repo for how to run: https://github.com/marbl/canu/issues/1731

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Thank you!

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