Comments (4)
olekto
commented on September 26, 2024
1
What kind of fish is this? We see similar issues with codfish, and the problem is that these fishes have a lot of short tandem repeats (microsatellites) which do not agree with PacBio sequencing much. What you get is regions of good coverage, and regions of really poor or no coverage, basically incomplete coverage of the genome. It will be hard to assembled such a dataset. It might help with increasing coverage (but we haven't explored this fully) and Revio might also help (different consensus algorithm, so might recover more bases than Sequel).
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chhylp123
commented on September 26, 2024
The FAQ here might be helpful: https://hifiasm.readthedocs.io/en/latest/faq.html#why-does-hifiasm-stuck-or-crash
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juliayork
commented on September 26, 2024
It is indeed a codfish! Okay, thanks for the tips. I'm going to send you an email shortly. If you don't mind, maybe we can stay in contact about this issue.
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olekto
commented on September 26, 2024
Sure, @juliayork, send me an e-mail at [email protected], and we can chat further.
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Related Issues (20)
- Mitigate Overlapping Sequence Assignments in Haplotypes HOT 3
- Help!!! Segmentation fault (core dumped) HOT 1
- Question about the depth of ONT ultra-long reads HOT 1
- Homotetraploid, super-large genome, with different parameters, the size of p_utg varies greatly？ HOT 2
- setting K parameter in yak HOT 2
- how to make the correct genome size estimation for allotetraploid species? HOT 2
- Possible missing one haplotype in human assemblies HOT 2
- No haploid.gfa files output in trio-binning mode HOT 3
- Hifi + Hi-c + ONT assembly fails
- In Trio-binning, always more on hap1 despite (almost) same sequences for paternal and maternal
- discontinuous assembly with shorter pacbio hifi reads but high coverage HOT 2
- 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
- missing 8Mb sequences in the assembly HOT 6
- Empty haplotype 2 gfa files by ONT integration HOT 1
- Basic Question About HiFi Input HOT 3
- Spend too long times to run hifiasm HOT 6
- Switch error on X and Y chromosome HOT 2
- *.ovlp.bin file HOT 1
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