The reason for low N50

[WagKing]

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]

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.