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borenstein-lab / microbiome-metabolome-curated-data

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Version of SBDI Sativa curated 16S GTDB database used #4

Closed MaximilianBaumgartner closed 9 months ago

MaximilianBaumgartner commented 9 months ago

Thanks a lot for providing this awesome resource !

I would like to merge some of my own 16S data, for this I would need the exact version of the SBDI Sativa 16S database that has been used (there are Version 1-5, with "1genome", "5genomes" and "20genomes" assignTaxonomy and addSpezies).

https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077

Did you use the dada2 assignTaxonomy function with standard parameters and these databases +then remove the species classification or modify the database beforehand and remove the species in the fasta names ?

Cheers, Max

efratmuller commented 9 months ago

Hi Max!

The specific file I used with DADA's assignTaxonomy was gtdb-sbdi-sativa.r07rs207.1genome.assignTaxonomy.fna.gz from version 5. I now also noted the version number and the file name in the Wiki.

As for your second question about how I ran the assignTaxonomy function, the exact script I used can be found here: https://github.com/borenstein-lab/microbiome-metabolome-curated-data/blob/main/scripts/data_organization/load_original_data/asv_assignTaxonomy_gtdb.R. I basically ran the assignTaxonomy function as is, and later slightly edited the format of species names, but I did not remove anything from the sbdi database itself. I hope that answered your question but let me know if it didn't.

Best, Efrat

MaximilianBaumgartner commented 9 months ago

Thank you Efrat for the lightning fast reply, this is exactly the information I needed !

Have a nice day and greetings from Austria, Max