Are the sequences in the QIIME2 database of SILVA reverse-complement

[nmgduan]

Hello, please check the following link of the QIIME2 reference databaseQIIME in SILVA.

The bases in the QIIME2 reference database of SILVA version are ATCG, but the bases in the SILVA reference database are AUCG. Therefore, before buliding the QIIME2 reference database of SILVA version, do you reverse complement the SILVA reference (AAGGUUCC→GGAACCTT) or just complement these reference (AAGGUUCC→TTCCAAGG)?

Thanks in advance!

Mort

[Nicholas_Bokulich]

Hi @nmgduan ,

@nmgduan

please check the following link of the QIIME2 reference databaseQIIME in SILVA.

That has not been updated for some time... the latest release there is 132, which is a few years old.

More up-to-date QIIME 2-formatted versions of the SILVA database are available on the QIIME 2 website:
https://docs.qiime2.org/2021.11/data-resources/

The original SILVA sequences consist of RNA, not DNA, so these are reverse transcribed to create the DNA sequence reference database available in the QIIME 2 resources (AAGGUUCC→AAGGTTCC).

You can see a full description of the steps used to create the QIIME 2 formatted versions of the SILVA database here (see the section "Getting SILVA data: Hard Mode" to see the full details):

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for constru…