18S reference dataset

[Fra (Francesco)]

Hello community,

I am working with an 18S dataset and I am looking for alternatives to the silva one. Is anyone aware of any good 18S reference dataset?

Cheers
Francesco

[colinbrislawn (Colin J Brislawn)]

Hello Francesco,

Silva is the most common and probably the best. But you could also check out PR2 if you are interested in 18S from Eukaryotes.

pr2database/pr2database

Colin

[emmzee]

Hey @colinbrislawn, is there anyway to use any of these two databases as reference databases in QIIME/QIIME2?

[Nicholas_Bokulich]

@emmzee

is there anyway to use any of these two databases as reference databases in QIIME/QIIME2?

Of course! Any reference sequence database can be used with QIIME 2, provided you format the database correctly. In fact, the PR2 database was made available in QIIME 2 format a while back by another forum user:

Qiime2 compatible oceanic databases - PR2 and Phytoref

Recently I was working on a project that requires tax assignment of oceanic samples using Bayesian classifier, but the main databases we used, PR2 and Phytoref, are not in the format compatible with Qiime2, so I just went ahead modified them and trained the classifier for Qiime2 use. If anyone also need to use these databases please feel free to download.

[Fra (Francesco)]

Thanks everyone, the PR2-R dataset classified many more ASVs at a much deeper taxonomical rank compared to the silva one.

Cheers
Francesco