Adding the PR2 database to improve detection and classification of eukaryotes?

[pjmramond]

Dear people from the mTAGs software/pipeline,

First of all thank you for this amazing program, mTAGs works wonders to get preliminary information on the taxonomic diversity of metagenomes, it's easy to use and very insightful!

I have noticed that eukaryotes may be under-represented in mTAGs in comparison with techniques based on read-recruitment by eukaryotic genomes. In turn, many fragments in mTAGs seem unaligned or unassigned.

I was wondering whether increasing the number of reference eukaryotic sequences could improve the detection and the classification of metagenomics eukaryotic rRNA fragments? In that case, do you think it possible/feasible to include the PR2 database as a component of mTAGs in the same manner as the Silva database? Merging them or having a second option more specific for eukaryotes?

I am mainly asking out of curiosity, maybe there is a reason that makes this not feasible or potentially not relevant. In any case happy to help or discuss this further!