How to get coverage depth information in the GFA? about hifiasm HOT 5 CLOSED

In each S-line of gfa, the "rd:i" indicates the coverage. For example,

S atg000001l * LN:i:43560 rd:i:12

The coverage of atg000001l is 12. We will upload a detailed manual soon.

from hifiasm.

Thanks for your reply, it is very useful. In my current hifiasm assemblies I notice that (in the raw utg gfa) many unitigs have coverage value indicated as zero in the "rd:i" field. This makes me wonder how hifiasm calculates the coverage values: could you provide some more details about it?

from hifiasm.

Hifiasm uses the reads of A-line to calculate coverage and considers contained reads at once. "rd:i" field is reliable for long contigs but might be not such reliable for short contigs.

from hifiasm.

Is it necessary to filter those contigs with zero coverage? I find quite a lot of them in my assembly

from hifiasm.

Is it necessary to filter those contigs with zero coverage? I find quite a lot of them in my assembly

How long and how many reads in these contigs? Could you please give me a few examples?

from hifiasm.