anvi-estimate-scg-taxonomy results differ from GTDB-Tk results

[Nastassia Patin]

Hey anvi'o team,

When running MAGs through anvi-estimate-scg-taxonomy (following anvi-run-scg-taxonomy of course) I often find that MAGs have no taxonomy assigned to them at all, even at the domain or phylum level. When I run these same MAGs through GTDB-Tk on KBase, they get taxonomic assignments down to the genus level. Do you know what might be causing this discrepancy? I only work with high-quality MAGs (completeness - 5 X redundancy > 40) and have updated anvi'o to the latest version.

Thanks,

Nastassia

[A. Murat Eren]

Interesting. If you use anvi-split to get a contigs database specific to that MAG and send it here, perhaps we can take a look :)

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A. Murat Eren (Meren) | he/him
http://merenlab.org :: twitter

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[Nastassia Patin]

Here's one example of a MAG that had this result. I didn't use anvi-split to generate it, though; I used anvi-gen-contigs-database. 

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Dr. Nastassia Patin

Postdoctoral Associate

Cooperative Institute for Marine and Atmospheric Studies

University of Miami/NOAA

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[A. Murat Eren]

Hey Nastassia,

You get no taxonomy because none of the ribosomal proteins is similar to anything in GTDB with more than 90% amino acid sequence identity. If you lower it to 80% with,

anvi-run-scg-taxonomy -c S2C3309-contigs.db --min-perc 80

Then the closes taxon is estimated to be the following:

So it is basically too novel to be quickly associated with anything confidently using quick-and-dirty approaches, and a tree-based approach like GTDB-Tk is essential to have a better idea about its place in the tree of life :)

Best,

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A. Murat Eren (Meren) | he/him
http://merenlab.org :: twitter

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[Nastassia Patin]

Got it, thank you! I didn't realize GTDB-Tk used phylogeny instead of ribosome protein % identity. Makes sense that a lot of them are Planctomycetes then, too. 

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