Hifiasm coverage rd:i:0

Question

[ccruz]

Hello,

I am currently trying to assemble de novo genomes for different algae species using HiFi-only Hifiasm. I am a bit confused because when I inspect the assembly graph of primary contigs (prefix.p_ctg.gfa) I see that some contigs have a read coverage of 0 (rd:i:0). However, the .gfa file does show some reads which are used to construct these contigs.

What does this mean?

Thank you! :)

Answer 1

[shelkmike]

See https://github.com/chhylp123/hifiasm/issues/467 . "rd:i:n indicates the coverage of this contig is n+1. As such for the contigs with rd:i:0, it is likely that there is only one HiFi read supporting them."

[ccruz]

Thank you! However, I have contigs where the .gfa file looks like this:

rd:i:0

A ptg000476l 0 + m64093_221119_214749/117572606/ccs 0 7024 id:i:5810622 HG:A:a

A ptg000476l 4762 - m64093_221119_214749/32901708/ccs 0 11223 id:i:5006894 HG:A:a

A ptg000476l 4957 + m54274Ue_221118_200412/4786700/ccs 0 14190 id:i:32239 HG:A:a

A ptg000476l 6810 + m64093_221119_214749/131663382/ccs 0 16387 id:i:5943723 HG:A:a

A ptg000476l 8996 + m54274Ue_221118_200412/53215868/ccs 0 15221 id:i:380415 HG:A:a

A ptg000476l 9821 + m54274Ue_221118_200412/51970766/ccs 0 16640 id:i:370682 HG:A:a

Doesn't this mean there are 6 reads supporting it?