QIIME2-Compatible Database for AMF Taxonomy Assignment – Issues with SILVA Lineage Depth

[Nicholas_Bokulich]

Hi @Salma_Sarker ,
Welcome to the forum!

I am not sure about an AMF-specific database for 18S (though some users have posted about using MaarJAM database with QIIME 2, so that might be one to check out). But I can answer your second question:

@Salma_Sarker

Alternatively, is there a recommended way to simplify or map long SILVA taxonomies to the standard 7 levels in a reproducible manner?

Yes, you can use the RESCRIPt plugin to parse the SILVA taxonomies (and choose whichever ranks you wish; default is the standard 7). See this tutorial for more 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 construc…

Good luck!