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 (#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!