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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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Suggestions on using --keep haplotypes #709

Closed riyasj327 closed 6 days ago

riyasj327 commented 3 weeks ago

Greetings,

Thanks for this wonderful tool! I have been using flye with --keep haplotypes option and then later hapdup for getting the diploid assemblies. I am wondering if it is suggested to use --keep haplotypes if running hapdup afterwards or it doesn't really matter?

Any insights on this would be really helpful!

thanks, Riya

mikolmogorov commented 6 days ago

Hi Riya,

For Hapdup, you need a collapsed assembly, so it is better not to use --keep-haplotypes.

riyasj327 commented 6 days ago

thank you so much! @mikolmogorov