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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
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Applicable for Eukaryotes? #25

Open morgansobol opened 5 years ago

morgansobol commented 5 years ago

Hello,

I was wondering if this program can be used for small eukaryotic genomes (<35 Mb) with less than 10% repeats?

Thanks, Morgan

cjain7 commented 5 years ago

It will surely run and give some distance values. Right now I can't comment on accuracy as we didn't benchmark it on eukaryotic genomes. Also I am not sure what are reliable metrics to compare/benchmark against. If you know it and can do couple of runs to test, I would be curious to see how it goes.

One assumption that is made during ANI computation is that all base-pairs are coding. This might be not be true for your genomes I think.

morgansobol commented 5 years ago

There was nothing reported in my output directory and the matrix file was all N/As.