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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Using HiFiasm for captured HiFi sequencing data #221

Open Redmar-van-den-Berg opened 2 years ago

Redmar-van-den-Berg commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Thank you so much.

Redmar-van-den-Berg commented 2 years ago

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

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chhylp123 commented 2 years ago

That's fantastic. Thank you so much.

wangBiojin commented 3 months ago

Hi,

I am working on the captured HiFi sequencing data now. how about your captured HiFi sequencing data? Did you assemble the contigs using hifiasm? how did you resolve the peak problem? Could you please give me some advice? Thanks!