Contradiction on Taxonomy Check Status

[alvanuffelen]

Not sure if I am at the right place for this issue, but there seems to be some contradiction on the Taxonomy check status of some assemblies.

Based on ANI page , the status Below-threshold-match is considered Inconclusive, and Below-threshold-mismatch is considered Failed.
However, in the ANI README, it is stated that both Below-threshold-match and Below-threshold-mismatch are considered Inconclusive.

But looking at some assemblies, all combinations occur:
Below-threshold-match and Inconclusive -->https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000022965.1/
Below-threshold-match and Failed --> https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002953655.1/
Below-threshold-mismatch and Inconclusive --> https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000010165.1/
Below-threshold-mismatch and Failed --> https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_023205975.1/

[ericcox1]

Hi @alvanuffelen,

Thanks for opening this issue. I agree that this could be clearer. I'm going to update the ANI documentation page to indicate that for both taxonomy check statuses, inconclusive and failed, all of these best match statuses are possible: below-threshold-match, low-coverage, lineage-match, below-threshold-lineage-match, mismatch, and below-threshold-mismatch.

Best,
Eric

[alvanuffelen]

Hi @ericcox1

Thanks for the reply!

How is the taxonomy check status determined if both can have those best match statuses?
And is the ANI README documentation then not correct if the ANI documentation page will state something else?

[ericcox1]

Hi @alvanuffelen,

We are still considering the updates to the online documentation and hope to get those done soon. I forwarded your questions to the team that runs the ANI analysis and I'm sharing their response to your question below.

How is the taxonomy check status determined if both can have those best match statuses?

Best match status is only one of the factors that determines the taxonomy check status. Other factors can include the number of assemblies and type assemblies that are available from the same species, the coverage of the assembly vs. the type strain and vice versa, and the quality metrics for the assembly in question.

Best,
Eric