Can silva database be used in protist taxonomic assignment?

Library Support Silva
1

Hi, I want to profile the protist community in the rhizosphere, can I use silva database as listed following?

https://data.qiime2.org/classifiers/sklearn-1.4.2/silva/silva-138-99-nb-classifier.qza

2

Hi @jiakang_yin,

Yes. the SILVA SSU contains data from both the 16S and 18S gene sequences, while the SILVA LSU contains data for both 23S and 28S.

You can also use RESCRIPt to pull reference data from specific databases that might contain these taxa, and construct your own classifier. Check out the following RESCIPt actions:

  • qiime rescript get-pr2-data --help
  • qiime rescript get-eukaryome-data --help
  • qiime rescript get-midori2-data --help
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3

Many thanks! :folded_hands: I will explore the RESCIPt.

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