blob plot to understand hifiasm haplotype assemblies

[cahuparo]

Hi @arangrhie ,

Thanks for developing this tool set. I wanted to ask you a question about interpreting blob plots and overall methodology.

I am working with a diploid highly heterozygous (~100Mb) genome (oomycete). We don't have at the moment progeny (f1) to built trio assemblies. We also don't have Hi-C data. But we were hoping to obtain close to T2T assemblies. We produced ONT R10 simplex reads and follow this workflow:

Raw FASTQ ONT reads > HERRO correction > hifiasm

Hifiasm produces phased haps but I want to make sure that these haps phased correctly, or that at least I could trust their assignment. So I used Merqury to test this using this command:

merqury.sh illumina_PE_read_kmer_db.meryl hap1_assembly.fa.gz hap2_asesmbly.fa.gz haps_merqury

#then I ran the hap_blob.sh like this:
bash hap_blob.sh hap1_assembly.meryl  hap2_assembly.meryl hap1_assembly.fa.gz hap2_assembly.fa.gz haps_merqury

This produced this plot:

Can I trust this blob plot to understand the quality of the haplotype assemblies?

Thanks,

Camilo

[arangrhie]

Hello, please read the wiki.
For phasing evaluation, Merqury relies on hapmers - inherited parental specific kmers, usually obtained from parental illumina/short reads.

Best, Arang