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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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The reason for low N50 #310

Open WagKing opened 1 year ago

WagKing commented 1 year ago

Hi,I want to know the reason for the low N50.Is one of this: 1、low read depth, and what is the minimum read depth to extend one contig? 2、if a het area can affect contig extend? 3、if a repeat area can affect contig extend? or any other reason for it?

thank you very much.

chhylp123 commented 1 year ago

Sorry I missed your issue... Yes, all these issues will affect the results. Another potential issue is the coverage dropout. For example, HiFi reads is more likely to have coverage drop in the GA-repeat regions.