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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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No haploid.gfa files output in trio-binning mode #636

Open tzjingyang opened 3 months ago

tzjingyang commented 3 months ago

Hi, I have HiFi reads, ONT-reads, HiC reads, and parents illumina short reads. So, I ran hifiasm with trio-binning mode to conduct haplotype assembly with the code 'hifiasm -o prefix.asm -t 32 --ul ont-reads.fa.gz --h1 hic-1.fa.gz --h2 hic-2.fa.gz -1 pat.yak -2 mat.yak Hifi-reads.fa.gz'. However, the output didn't have the two haploid gfa files. The outputs are as follows:

1712889273430

There's no error in log file. Could you give some advices? Thank you for your assistance.

tzjingyang commented 3 months ago

The description provided earlier was incorrect. The log file displayed 'Segmentation fault' at the end. Is it appropriate to use these sequence data together in hifiasm trio-binning mode? Hope you will give me some advice on using these data to assembly haplotype genome. Thanks!

chhylp123 commented 2 months ago

Sorry for the late reply @tzjingyang. Hifiasm cannot use Hi-C and trio phasing at the same time. In most cases, it would be better to use trio-binng with yak index since trio-binning is more reliable than Hi-C phasing.

tzjingyang commented 2 months ago

Thanks. Then, where should I use the hi-c data to get exact results? or the hi-c data only used in scaffold steps.