What's the best analysis process with 1.HiFi long reads; 2.Hic reads; 3.Paired-end reads (Trio)

[jackzhong1995]

Hello! When i have 1.HiFi long reads; 2.Hic reads; 3.Paired-end reads (Trio).Is there any flowchart comand line to get the best assembly?

[chhylp123]

If you have trio data, HiFi+trio would be better.

[jackzhong1995]

Thanks for your quickly reply! You mean like these comand line ? yak count -k31 -b37 -t16 -o pat.yak <(zcat Father1.fq.gz) <(zcat Father2.fq.gz) yak count -k31 -b37 -t16 -o mat.yak <(zcat Mather1.fq.gz) <(zcat Mather2.fq.gz) hifiasm -o raw.asm -t 32 -1 pat.yak -2 mat.yak Hifi.fasta.gz