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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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AllHiC on Hifiasm assembly #112

Open sandipmkale opened 2 years ago

sandipmkale commented 2 years ago

Hello,

Thanks for great tool. I have question regarding development of phased assembly. I used hifiasm to generate haplotype level contain assemblies. As the phases are interchanged in the hifiasm assembly, can I merge the hap1.p.ctg.fa and hap2.p.ctg.fa and run the AllHiC to generate phased assemblies?

Thanks and regards

Sandip

tangerzhang commented 2 years ago

Yes, It should be totally OK to merge the hap1.p_ctg.fa and hap2.p_ctg.fa and run ALLHiC for haplotype phasing. Alternatively, you can also use p_utg.fa for ALLHiC phasing if you do not have trio data.

sandipmkale commented 2 years ago

Thanks alot for reply. The haploid genome size is 2.5 Gb, but the p_utg.fa file is 4.5 Gb so around 500 Mb data is merged in the p_utg.fa file. I run the AllHiC but didn't get satisfactory results. I calculated coverage for each units using the pipeline mentioned in the tea genome (Nature Genetics) paper but the maximum depth in *read_depth.txt file is 1. so decided to merge hap1.p_ctg.fa and hap2.p_ctg.fa.