Looking for Pre-trained Silva Classifier (V3-V4)

Dear all,

Does anyone trained the naive-bayes classifier based on Silva reference database (V3-V4 region) ? I ran taxonomy classification using full length pre-trained classifier from qiime2 resource page and it was killed due to memory error. I tried to train self-customized classifier as well, but the action was killed due to memory error as well. Thus, I would like to ask the good deed from qiime 2 users to provide the Silva-based classifier by which the reference reads were extracted by 341F & 805R degenerate primers.

Thank you.

-Benedict-

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Hi @Benedict,
That would be useful indeed, but in the meantime if you are unable to get the specific classifier you need, you can always use the full-length classifier available and play around with the parameters as suggested here. Basically leaving the --p-n-jobs to its default 1 and starting with smaller chunk size using --p-reads-per-batch INTEGER RANGE of say 1000. It’ll take longer but you may not run into the memory issue. Sorry in advance if you’ve already tried these and they haven’t worked.

Hi @Benedict

I have uploaded a silva V3V4 classifier available at: https://drive.google.com/file/d/1CvmZ1ONAi1dl2_TnzVm4Hc4gG6eSz7a5/
Alos, the training details can be found here: https://github.com/Jiung-Wen/q2-silva-V3V4classifier
Hope it helps.

Best,
Jiung-Wen

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