Run purge_dups with PacBio hifi reads and HiCanu assembly
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
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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
Thank you!