QIIME compatible taxonomic databases help

(Ben) #1

Hello everyone,

If you are using QIIME, can you guys share me with your latest taxonomic databases (compatible databases). As you know, some of databases coming with Qiime are little bit old. I am not sure if the taxonomic databases format would be same for Qiime 1 and 2. I also have a manuscript coming back using QIIME1. If you can share with me your latest Qiime compatible databases for Qiime 1 and 2 would be great. Particularly, I am interested in these three RDP (16S), Silva (18S) and Unite (fungi).

Everyone is welcome to post.

Can you follow this format:

For example:

RDP database – latest QIIME compatible version is XXX.

QIIME 1 compatible version download link is (http://…)

QIIME 2 compatible version download link is (http://…)

I know database website can update very quickly. Please share with me (us) the version that you are currently using.

Thank you,
Ben

(Colin Brislawn) #2

Hello Ben,

Good to hear from you again. I’m glad you are making the transition to Qiime2. Welcome! :qiime2:

This page lists the current Qiime 2 databases. This should include some of the links that you want:
https://docs.qiime2.org/2019.1/data-resources/#taxonomy-classifiers-for-use-with-q2-feature-classifier

Colin

(Ben) #3

Thanks. Would QIIME 1 and 2’s databases are same format?

Does anyone get trouble from reviewers complaining about GreenGenes database old

(Matthew Ryan Dillon) #4

I will add to this list, there are a few other pretrained classifiers representing other databases to be found here:

https://forum.qiime2.org/c/community-contributions/data-resources

(Ben) #5

Thank you guys.

Are the databases format same in QIIME 1 and 2?

BTW, I know the official database updated quite quickly? I know lots of QIIME users here. Can you guys recommend the popular versions of Silva, RDP and UNITT, respectively. (They don’t necessarily be most updated, but the manuscripts reviewers won’t complain about they are old)

(system) closed #6

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