Comments (5)
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.
Related Issues (20)
- Possible missing one haplotype in human assemblies HOT 2
- No haploid.gfa files output in trio-binning mode HOT 3
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- Is x20 of Hifi data enough to construct draft assembly of 6.5Gb genome? HOT 1
- line 8: 110334 Aborted(core dumped) HOT 1
- Ultra Long intergration failed: no output for UL kmer counting HOT 3
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- Basic Question About HiFi Input HOT 3
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from hifiasm.