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Basic Question About HiFi Input

Open foreignsand opened this issue 2 months ago • 3 comments

I've scanned the Docs and the Issues and can't see anything about which reads are used from PacBio HiFi sequencing output. Should the total ccs reads located in the 'reads' directory be used? Or the quality filtered reads? I have Q20, Q30, Q40, and Q50 ccs reads I could use.

Another question I have is, if the total ccs reads are used, can the quality filtered reads serve any purpose? Is it possible to do multiple passes with hifiasm initially using the total reads and then using Q30 reads for polishing?

Many thanks!

Cheers, Emily

foreignsand avatar May 02 '24 21:05 foreignsand