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aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
http://atcgn.com:8080/quarTeT/home.html
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Could I generate haplotype-resolved assembly using AssemblyMapper? #13

Closed hui-liu closed 1 year ago

hui-liu commented 1 year ago

Hi,

Thanks for developing the nice package.

(1) I have two contig-level phased assembles, including {prefix}.bp.hap1.p_ctg.fasta and {prefix}.bp.hap2.p_ctg.fasta, generated by hifiasm with HiFi reads. If I have a closely related reference genome (ref.fasta), should I run the AssemblyMapper as following commands?

python3 quartet.py AssemblyMapper -r ref.fasta -q {prefix}.bp.hap1.p_ctg.fasta python3 quartet.py AssemblyMapper -r ref.fasta -q {prefix}.bp.hap2.p_ctg.fasta

(2) In addition, if have a closely related reference genome that is haplotype-resolved (ref_hapA.fasta and ref_hapB.fasta), I am wondering if could I generate a haplotype-resolved assembly based on the closely related reference genome?

Thanks!

Echoring commented 1 year ago
  1. YES.
  2. You can merge the two reference to one ref.fasta, and do the same as (1). Half of reference will fail to be mapped (or mapped by only some short contigs), indicating the belongings.