Question about preparing FASTA Input Files for Assessing Haplotype-Resolved Genomes of Autotetraploid Species Using Merqury

[kedduck]

Hello, arangrhie,

Merqury has proven to be an excellent tool for evaluating genomes.

I currently possess a haplotype-resolved genome from an autotetraploid species, which includes four haplotypes. In order to validate the quality of this genome assembly, I would like to utilize Merqury. I have reviewed a previous issue on GitHub (https://github.com/marbl/merqury/issues/108), but it did not provide much insight into my specific scenario.

My question is: Should I include the entire genome assembly in a single FASTA file as input, which would include both the chromosomal sequences and the unscaffolded contigs?

Thank you for your assistance.

[arangrhie]

Hi @kedduck,

Do you have the parental genomes / kmers? Can you split your assembly to mat / pat assemblies? I have seen that some autotetraploids were coming out nicely as diploids when coloring on the assembly graph.

I have polyploid Merqury in my back-burner, will take me some time to implement... can take a crack, but don't wait for me. In the mean time, try this suggestion to plot ~8 copy numbers in the plots.

Best, Arang

[kedduck]

Thank you for your answer. I am sorry for not providing detailed information. My species is an autotetraploid, and the diploid ancestral species also has a assembly. However, I believe that over time, there have been many differences between the tetraploid and the diploid.

I have an interesting idea. For example, if I have two autotetraploid species with the same genotype S1 S2 S3 S4, then their hybrid offspring might have the genotype S1 S2 S3 S4. So, can I theoretically consider my species as both the male and female parent at the same time?

Looking forward to your reply. Thank you!

[chklopp]

Hi, One way to produce qv and completeness for polyploid is to produce the values two by two for haplotype couples and then merge all the haplotypes and produce the values for the merged file. You will then have all individual haplotype values as well as total haplotype values.