Sequence divergence of whole genomes

Question

[Colaptes]

Hello,

I sequenced and assembled the genomes of two closely related species, and I would like to calculate the pairwise sequence divergence between the two whole genomes. I have done this for many orthologous genes extracted from the genome, but now I would like to align the whole genomes and calculate overall divergence. The genomes are in fasta format.

I know how to align the genomes and get a sam/bam file, and I know how to calculate sequence divergence between aligned fasta entries, but I am not sure how to link the steps. Is there a good way to get fasta-format alignments for whole genomes, or other ways to calculate their sequence divergence? (Bonus if there is a way to exclude coding regions stored in GFF files!)

Thank you!

Answer 1

[Mensur Dlakic]

Would you be interested in whole-genome average nucleotide identity? If so, this program will do what you want:

https://github.com/ParBLiSS/FastANI

It is fast and does not require any external programs.

[Colaptes]

Thanks! I would definitely be interested in something like that. I should have mentioned that my genomes are eukaryotic (~1 Gb, ~10% repeat), and it seems that the developers of FastANI warn that it is not tested for use on eukaryotic genomes.