Using HiFiasm for captured HiFi sequencing data

[Redmar-van-den-Berg]

I'm working on a project that uses targetted HiFi sequencing of pharmacogenetic genes to deliver personalised advice regarding medicine dosage to patients. I am trying to use HiFiasm to do a phased assembly of the genes of interest, but I either get many small contigs, or phase switching within the genes, which makes the alleles called unreliable. Do you have any advice on how to use targetted data with HiFiasm? When I look at the Kmer plots for my data (multiqc_report.zip), I do not see the two peaks that are mentioned in the HiFiasm documentation.

[chhylp123]

Actually, we are also looking forward to seeing if hifiasm can work on targetted datasets, but so far we don't have such datasets for debugging. If you can share some of them with us, it would be very helpful.

[Redmar-van-den-Berg]

We did run our capture protocol on one of the GIAB trio's, so we can share that data with you in the new year.

[chhylp123]

Thank you so much.

[Redmar-van-den-Berg]

This is the best sequencing batch we have for the GIAB trio with our protocol:

mother father child

[chhylp123]

That's fantastic. Thank you so much.