Taxonomy assignment with custom COI database - odd/wrong classifications?

[SoilRotifer (Mike Robeson)]

Hi @elaine-shen,

There could be a variety of reasons for this. Most common is inconsistent taxonomic annotations which 'confuse' the classifier...

I would suggest trying out the CO1 reference databases from @devonorourke:
BOLD references:

Building a COI database from BOLD references

Citations: If you use the following COI resources or RESCRIPt for COI database preparation, please cite the following: Michael S Robeson II, Devon R O’Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich. RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. bioRxiv 2020.10.05.326504;…

The files are available here:

Building a COI database from BOLD references

Hi @smayne11, thanks for your question. I think you should give the ANML classifier a shot. I'd be curious to see how many of your sequence variants are classified (or unclassified), and among those with some taxonomic labels, what fraction are being assigned Family, Genus, or Species-level information. If the classifier isn't working for you and you want to generate your primer-specific classifier starting from the broader BOLD sequence and taxonomy files now hosted by QIIME2 here: https://…

and the NCBI approach here:

Building a COI database from NCBI references

Citation: If you use the following COI resources or RESCRIPt for COI database preparation, please cite the following: Michael S Robeson II, Devon R O’Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich. RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. bioRxiv 2020.10.05.326504; d…

There is another CO1 reference database maintained by the Porter Lab available here.

I think it would be a good to compare these reference databases to your existing one.

-Cheers!
-Mike