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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
GNU General Public License v3.0
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Does PiCrust2 generate 16S taxonomic classifications using your reference tree? #321

Closed carmennns2 closed 5 months ago

carmennns2 commented 1 year ago

Hi,

Thank you for the great tool. I'm new to picrust2 and wanted to ask two questions (I apologise if their silly). I read the paper but am still slightly confused.

  1. picrust2 uses its own reference tree as a database. Does picrust2 also generate 16S taxonomic classifications?

  2. The output of add_description generates a path_abun_contrib.tsv file. Can I confirm the values in the "taxon" column (e.g. ASV_1, ASV_2, ASV_3...etc) is the same ASV as in my input file to run picrust2? (or is this a different ASV generated by the reference tree?).

Thank you so much (: Carmen

gavinmdouglas commented 1 year ago

Hi there,

  1. No it does not perform taxonomic classification, although I have heard rumblings of other tools out there that I am not involved with for placement-based classification. Not sure if anything is available yet though!

  2. That will be the same ASVs as you input originally - no new ASVs will be added.

Cheers,

Gavin

carmennns2 commented 1 year ago

Thank you so much (:

R-Wright-1 commented 5 months ago

I am just closing this as it doesn't seem that there's an issue. Please let me know if it needs to be reopened.

I'll also note incase anyone else finds this and is interested, the GTDB toolkit does offer tree-based classification for Metagenome Assembled Genomes. There are also some third-party tools that can be used for 16S classifications, but I haven't looked in any great detail to see how these are performed.