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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Can hifiasm output assembly reads coverage for each utg？ #180

Closed 865699871 closed 3 years ago

865699871 commented 3 years ago

Can hifiasm output assembly reads coverage for each utg？ like
1630829021(1)

chhylp123 commented 3 years ago

rd:i: is the coverage. See https://hifiasm.readthedocs.io/en/latest/interpreting-output.html#output-file-formats .

865699871 commented 3 years ago

Thank you for your answer. We found the rd:i of some utg are 0. 1630916346(1)

What strategy used for hifiasm to assign read coverage？Why zero occur？

chhylp123 commented 3 years ago

It is calculated by the reads coming from the same contig/unitig. rd:i:X indicates coverage of X+1.