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Published 20 hours ago • verified publisher icon ParBLiSS

For plant genome

Open yilunhuangyue opened this issue 4 years ago • 4 comments

Hi, I used FastANI for several plant genome and did get results. The ANI values were higher for species with closer genetic relationship. But I am not sure if the ANI values meaningful? Thanks a lot for your advices

yilunhuangyue avatar Aug 14 '20 03:08 yilunhuangyue

I've not benchmarked ANI values for eukaryotes. As far as I'm aware, fastANI output would need some post-processing to be consistent with standard phylogenetic distances. cc'ing @balabanmetin as he was also interested in extending ANI estimates for eukaryotes.

cjain7 avatar Aug 20 '20 03:08 cjain7

Hey @yilunhuangyue this is really perfect! has this been further developed for bigger genomes? or eukaryotes?

LandiMi2 avatar Aug 25 '22 12:08 LandiMi2

No, we didn't make progress on extending FastANI on eukaryotic genomes yet. Maybe others have looked into it.

cjain7 avatar Aug 26 '22 04:08 cjain7

Hey, @cjain7 thanks for the response. I have however tried to use this tool yesterday on a 650Mb two haplotypes of roughly the same. I tried to adjust --fragLen 50000. This worked for me and it calculated ANI to the end. Not sure if this is the right way to approach this for bigger genomes.

LandiMi2 avatar Aug 26 '22 06:08 LandiMi2