Run purge_dups with PacBio hifi reads and HiCanu assembly

Question

[scruffener]

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

[gconcepcion]

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

[scruffener]

Thank you!