Question: ANI software for comparing large eukaryotic genomes
0
gravatar for eduardodelarosa
4 months ago by
eduardodelarosa0 wrote:

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!

ADD COMMENTlink modified 4 months ago by 5heikki9.0k • written 4 months ago by eduardodelarosa0
2
gravatar for 5heikki
4 months ago by
5heikki9.0k
Finland
5heikki9.0k wrote:

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..

ADD COMMENTlink modified 4 months ago • written 4 months ago by 5heikki9.0k
1
gravatar for Mensur Dlakic
4 months ago by
Mensur Dlakic7.0k
USA
Mensur Dlakic7.0k wrote:

I suggest you try FastANI. Another option is pyani.

ADD COMMENTlink written 4 months ago by Mensur Dlakic7.0k
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