hifiasm
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chhylp123
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hi, I am using the allotetraploid plant species to assemble the genome. I have the 3 cells PacBio HiFi reads data to assemble the genome. I ran the code as...
Hi @chhylp123, I was wondering if hifiasm can run without PacBio Hifi reads. I only have Ultra long ONT reads and I am wondering if the newer flag (`-ul`) would...
Minimal changes that got this building and apparently working correctly on Apple silicon.
hi, developers, I am encountering an issue during the hexaploid genome assembly except ~3G with haplotype, but the results are larger. I used 2 cells hifi reads approximately 175G driverd...
Hi, I am assembling hifi CCS reads generated by the PacBio Revio instrument. When I run hifiasm (hifi only) I get no output files besides the .log file but there...
Hi, can you please describe the options '--dual-scaf' an d'--scaf-gap'. There is no description of it in the documentation. Is this for Hi-C scaffolding or ONT? Thanks, Theo
Hi, I'm assembling a 3 Gb diploid mammal, but we know it is likely to be quite homozygous. This is confirmed by the k-mer peak, and hifiasm "correctly" identifies the...
Hello @chhylp123 This is an assembly of plant material that was initially thought to be diploid, as shown in Figure 1. It was later found to be tetraploid, as shown...
Hello, I am using hifiasm to perform hifi-only assembly of a allopolyploid species. While the basic metrics are good (high N50, Complete BUSCO>98%), I got only 57% of Duplicated BUSCO....
Hello, I'm look into the meaning of the columns of the lines in GFA files. Although I've checked the links you recommended, such as https://hifiasm.readthedocs.io/en/latest/interpreting-output.html and https://gfa-spec.github.io/GFA-spec/GFA1.html, But I didn't...
