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CAMI-challenge / CAMITAX

CAMITAX: Taxon labels for microbial genomes
https://doi.org/10.1101/532473
Apache License 2.0
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Confidence values #12

Closed AlphaSquad closed 5 years ago

AlphaSquad commented 6 years ago

It might be useful to have some kind of confidence values of the tools (if they provide it internally). I have seen the following example for one of the (new) genomes: The LCA of tools was bacteria (TaxID 2), which was caused by a single conflicting assignment: Mash, Kaiju as well as Centrifuge all predicted a Psychrobacter, CheckM predicted bacteria, only dada2 predicted a Chryseobacterium which is of a different phylum than Psychrobacter. If the dada2 prediction is not really confident, one could decide to go with the matching prediction of the other 3.

abremges commented 6 years ago

Can you provide me with the genome ID please, such that I can manually inspect the assignments? I'm a bit surprised, because I already require a bootstrap support of 80/100 for Dada2 assignments.

abremges commented 6 years ago

(Also, it's not LCA but the lowest consistent assignment.) 😛

abremges commented 5 years ago

Not feasible to expose & individual tool assignments are available in the output folders.