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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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How to use HIC data in the hifiasm and allhic assembly strategies？ #135

Open naturalstay opened 2 years ago

naturalstay commented 2 years ago

Hi, Thanks for developing this useful tool. I assembled two haplotypes from a diploid plant using the hifiasm tool with HiFi and HiC data. Now, I use HiC data to anchor two haplotypes. You mentioned that anchoring them separately would be much easier.#99 Are haplotypes anchored separately using HiC data used by HiFiasm? This way the HiC data is used three times (HiFiasm and two anchors). Looking forward to your reply. Thanks.

tangerzhang commented 2 years ago

As far as I know, you can get two haplotype assemblies at contig-level from hifiasm if you specify the parameters --h1 and --h2, which take the Hi-C data as inputs. After that, you can get chromosomal-scale assemblies for the two haplotypes, respectively. And yes, you are right. Hi-C data is used three times if you are working this way.

Wenwen012345 commented 1 year ago

As far as I know, you can get two haplotype assemblies at contig-level from hifiasm if you specify the parameters --h1 and --h2, which take the Hi-C data as inputs. After that, you can get chromosomal-scale assemblies for the two haplotypes, respectively. And yes, you are right. Hi-C data is used three times if you are working this way.

Hello, @tangerzhang I would like to ask by the way. It seems to be full of chimeric contigs in my case. There is an extra large chromosome being built. Is it because of the "anchor together (2n chromosomes)" method used?