Hello,
I'm looking to accumulate as much publicly available 16S sequence data for a phylum of bacteria (generally referred to as myxobacteria).
At this point, I've downloaded all the sequences from NCBI. From what I've read, Silva uses sequences from NCBI so am not using that. I'm also downloading the GreenGenes database, although it looks like it is no longer up-to-date. Are there any other databases that I might be able to use that would have unique 16S sequences?
Appreciate the help.
Peter
All databases are interconnected and mostly NCBI has most of them just because several others are curated and has less frequent updates. So in my opinion NCBI and silva are very good source. You can try to download the GTDB 16S rRNA database.
I would have to get all the possible unique sequences I would pool all the sequence and simply discard the duplicates. But for amplicon sequencing or any other similar reference based analysis there is no need of such huge collection of sequences. Only a few sequences can also do the job.
Thanks. FYI - RDP said they should be back up and running in the coming weeks.
You can try MIMt (https://mimt.bu.biopolis.pt) since it has been tested against SILVA, Greengenes, RDP and GTDB using differente softwares (QIIME2, DADA2 and Mothur) and in all tests performed even a 50% better than the rest. Here you can find the publication: https://www.biorxiv.org/content/10.1101/2023.12.15.571851v1