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wwood / singlem

Novelty-inclusive microbial community profiling of shotgun metagenomes
http://wwood.github.io/singlem/
GNU General Public License v3.0
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Assignment of chlorplast RPs #51

Closed suskraem closed 4 years ago

suskraem commented 4 years ago

Hello,

I was wondering how chloroplast RPs are assigned with singleM. I don't think there is a category for chlorplasts in the database singleM uses. Are they assigned to Eukarya or maybe to Cyanobacteria?

Thanks a lot!

wwood commented 4 years ago

Hi, thanks for your interest.

They are meant to be Eukarya. ben

suskraem commented 4 years ago

Hello Ben,

thanks for your reply. What would be the taxonomic string for chloroplast RPs?

Thanks!

wwood commented 4 years ago

Hi,

In most cases they should be Eukaryota; Plantae, using either diamond or pplacer assignment methods. GraftM, which interprets the the pplacer results, does not require monophyly in the reference trees to assign taxonomy.

Let me know if that doesn't square with your observations. ben