Create NCBI database for identifcation with ITS region

[SoilRotifer (Mike Robeson)]

I forgot to mention you can try setting up a more generic queries... like:

Streptophyta:
--p-query "txid35493[ORGN] AND (ITS OR Internal Transcribed Spacer) NOT environmental sample[Title] NOT environmental samples[Title] NOT environmental[Title] NOT uncultured[Title] NOT unclassified[Title] NOT unidentified[Title] NOT unverified[Title]"

or

Embryophyta:
--p-query "txid3193[ORGN] AND (ITS OR Internal Transcribed Spacer) NOT environmental sample[Title] NOT environmental samples[Title] NOT environmental[Title] NOT uncultured[Title] NOT unclassified[Title] NOT unidentified[Title] NOT unverified[Title]"

etc...

More examples here:

Make 12S reference database using Rescript

Hi @Junli_Zhang, I’ve got quite a bit of experience in making 12S rRNA gene databases (e.g. for eukaryota, and metazoa). Hopefully, we can help. I agree with @Nicholas_Bokulich, there are things beyond our control when it comes to internet connections. Your query does not appear to result in that many sequences, but you can break it up into smaller downloadable chunks within the vertebrates. Here is a query you can use to download Gnathostomata: txid7776[ORGN] AND (12S OR 12S…

Building a COI database from NCBI references

Citation: If you use the following COI resources or RESCRIPt for COI database preparation, please cite the following: Michael S Robeson II, Devon R O’Rourke, Benjamin D Kaehler, Michal Ziemski, Matthew R Dillon, Jeffrey T Foster, Nicholas A Bokulich. RESCRIPt: Reproducible sequence taxonomy reference database management for the masses. bioRxiv 2020.10.05.326504; …

-Mike