Zhigui Bao

That's so great. Is the output sorted by read name? Another behavior is that chromap merge all the output after mapping. Count it can directly output to the stdout when...

Hi, @sfchen I have the same issue with @edgardomortiz . Did it have any progress or solution ? Here is the command I use ```shell fastp -w 6 -6 -i...

@sidorov-si You can assembly the whole HG002 HiFi reads or just one chromosome, and then grep the HiFi reads in the `*.p_utg.noseq.gfa` for pipeline testing. I have try assembly a...

Hi, Mike Thanks for quick reply. I already replace the paf with wfmash like the #86 , it perfectly scaffolded.

You can easily rerun with the bin file to get primary/alternative, dual assembly or trio/hic assembly if you use the same prefix

Yes, hifiasm will reuse all the bin files if they exist. But be careful if it is generated by a different version of hifiasm.

Thanks for the prompt reply and nice advices. I will take next extra filter step with miniprot gff3. I am totally agree with you about the annotation step. Cross-species protein...

For reference, it was hifiasm-based Arabidopsis thaliana. The query was taken from a TE annotation tool which they use for filter flase TE by protein-coding gene (https://github.com/oushujun/EDTA/blob/master/database/alluniRefprexp082813). It consists of...

Great!! I will filter out by that tag. But another issue still exists. Since the various annotation quality of different species assembly, it's hard to make a tradeoff between the...

Hi, Tao But for the assembly-based SVs calling, did `cuteSV` still cluster breakpoints? Since it is only one read in the sam, could it be possible for `cuteSV` to report...