Looking for pre-trained SILVA 138 V4 classifier for QIIME2 2024.10

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Hi everyone,

I am working on 16S rRNA gene V4 region analysis using QIIME2 2024.10 on a Windows machine with WSL (16GB RAM). I am looking for a pre-trained SILVA 138 99% OTU classifier for the V4 region with the following specifications:

  • QIIME2 version: 2024.10
  • Primers: 515F (GTGYCAGCMGCCGCGGTAA) / 806R (GGACTACNVGGGTWTCTAAT)
  • Reference database: SILVA 138 99% OTUs
  • scikit-learn version: 1.4.2
  • Sequencing platform: Illumina MiSeq

My computer has 16GB RAM and is unfortunately unable to train the classifier locally due to memory limitations. The process gets killed before completing.

If anyone has this classifier file (silva-v4-classifier.qza) or knows where I can download a compatible pre-trained version, I would really appreciate your help!

Thank you so much in advance!

Richa

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Hello Richa,

Thank you for the detailed post. Pretrained classifiers that work with Qiime 2024.10 are included on the data-resources page:

It looks like the specific combination you are looking for is not here. But some other classifiers are close!

For your consideration:
Silva 138 99% OTUs full-length sequences, which is full length instead of just V4.
Greengenes2 2024.09 from 515F/806R region of sequences, which is trimmed to the V4 region but is not SILVA.

Given your 16GB memory limit, trying a search-based consensus classifier is a good idea:

Let us know what you try next!

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Hello!

I have one trained with the same primers (just checked) and Qiime2 version, Silva 138.2 (did you mean the first release 138 with outdated taxonomy? Mine is trained on 138.2, with updated names).

Here is the link. All files are in the q2-2024-10/Silva138_2 directory, with V4 in the name (classifier, taxonomy and sequences).

Best,
Timur

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Hi Colin,

Thanks for your help and suggestions. This is helpful. I need to use Silva; I found one pretrained Silva 138 classifier in Github and I see one more reply here in which a pretrained version is shared-I will try using that. Thanks again for your time and sharing information.

Richa

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Thanks Timur! Just checked the link and found the directories. This is extremely helpful !

Richa

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