Taxonomic databases for sidle (Ampliseq pipeline, multiregion sidle option)

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Hi,
I am trying to use (nextflow) ampliseq pipeline (https://github.com/nf-core/ampliseq ) with the multi region option which use sidle. For the taxonomy step, sidle can use 2 readily databases (silva or GreenGenes2). Unfortunately, those databases have only 16S. I am working with ITS plant, rbcl plant, 12S bird and 12S mammal samples.

I would like to know if there is other available databases for sidle which could fit with my samples (ITS or Rbcl or 12S) ?
If this doesn't exist, could you advise me on how to make a customized database that works with sidle ?

Thank you in advance for your help!

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For ITS I've used the Unite-Database.

Unite is also supported by RESCRIPt, which can be helpful in building databases.

How many different amplicon regions did you target in total? ITS, rbcl, 12S for 3 total?

P.S. Welcome to the forums!

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Thank you very much for your kind and useful answer !

On your advice, I used Unite with my ampliseq pipeline. Unfortunatly, the taxonomy is wrong (I got Cercozoa sp. instead of plants). I blast on ncbi the ASV sequences and it matches with my plants. So I think there is maybe a problem with the Unite database I used. I will check this out.

Currently, I have 5 different amplicons. ITS and Rbcl which are made separatly (simplex PCR) and 12S + 2 16S which are made together (multiplex PCR). I guess that I will need to create 3 different databases ( one ITS, one Rbcl and one 12S + 16S + 16S). I'll take a closer look at how RESCRIPt works and keep you posted on my progress !

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