Available: Pre-trained classifier of V3-V4 (341F, 805R) region with gg_99

feature-classifier

(Mehrbod Estaki) #1

Hi folks,

In case anyone is interested I have a pretrained classifier on the V3-V4 region using the following primers:
341F: CCTACGGGNGGCWGCAG
805R: GACTACHVGGGTATCTAATCC
The primer set is taken from Illumina’s 16S library preparation protocol.

It was trained using the Greengenes 99_otu_taxonomy.txt using naive bayes method on qiime2017.12, its about 44MB.
If this is something you’d like to use let me know!
-Bod


Feature classifier
Training Feature Classifier
(Juan Díaz Carrasco) #2

Hi Bod,

I’m interested in the V3-V4 classifier you used. I have exactly the same primers pair in my data. I would also like to take a look on the commands you used, so I can try to reproduce it in my computer from the gg-13-8 full-length sequences database.

Thank you very much in advance!

ju4n


(Mehrbod Estaki) #3

Hi @ju4n_dc,

Here is a dropbox link to the classifier to download, let me know if you run into any problems. You can follow the exact commands within the provenance in the file to see what was exactly done.
Hope this helps!

-Bod


(Juan Díaz Carrasco) #4

Thanks Bod! It worked OK.

ju4n


(Nicholas Bokulich) #5

An off-topic reply has been split into a new topic: How to read provenance in an artifact file?

Please keep replies on-topic in the future.