Average Nucleotide Identity Calculation among bacterial genomes

Question

[Optimist]

Hi Folks!!!

Are there any tools which can be used to calculate the Average Nucleotide Identity (ANI) among the bacterial genomes.

I was trying to use Jspecies but there were various problems with it.

Can someone suggest ant tools to calculate ANI among various bacterial genomes (say 26)

Thanks a lot

Optimist

[bird77]

if you have an answer, please share it, i have the same problem.

[Joe]

You want ANI between ALL bacterial species?

Answer 1

[SciLand]

Try Pynai, available from https://github.com/widdowquinn/pyani

[Anand Rao]

Can this work equally well for non-bacterial genomes? In my case, I wanna try haploid fungal spore genomes. Your advice / thoughts?

Also, I wonder if this is compatible only with SGE scheduler or even others, like the SLURM I use, would you know Thanks!

[SciLand]

Hi Anand,

It should work for fungal genomes too. I am not sure if it is compatible with another workload manager. Please contact the developer of the 'pyani' package for the compatibility.