ANI software for comparing large eukaryotic genomes

Question

[eduardodelarosa]

Hi! I´m trying to do whole genome comparisons between mammalian species (all I need are percent identity values). Due to the large size of the sequences (roughly 20 GB each) I haven´t been able to find an algorithm that can parse them. So far the most promising seemed to be MUMmer and OAT (orthoANI), but they still have not given me any results as of yet. Any insight on the matter is most appreciated, thanks!

Answer 1

[5heikki]

This can be done very quickly with Mash. Read the docs and the paper and marvel how great stuff MinHash and representative sketches truly are. ANI is approximate to one minus Mash distance..

Answer 2

[Mensur Dlakic]

I suggest you try FastANI. Another option is pyani.