How can i custom the reference database that i want to use in QIIME?

Question

[antonioggsousa]

Hi everyone.

I'm starting to work with QIIME pipeline for 16S rRNA gene amplicons data analysis.

One of the drawbacks of this pipeline is the use of GreenGenes database which underwent the last update in 2013. So I would like to custom the reference database to use SILVAngs database instead of GreenGenes db.

I try to do this before but i couldn't get any successful result.

Someone can help me on this, please.

Thank you. Regards, António

Answer 1

[glihm]

Hi Antonio,

It may helps you: Making custom database (like green genes) for QIIME Closed-reference OTU picking.

Otherwise, I worked a lot with 16S rRNA gene amplicons and I did it directly with Usearch (http://www.drive5.com/usearch/). QIIME and MOTHUR are Usearch based and more user-friendly. Usearch is all in command line, but with the online tutorials and the documentation you can reach your goal I think.

Good luck !

[antonioggsousa]

Thank you a lot Wocka.

Actually I'm learning to use Usearch too because one of my goals is assess which is the best current pipeline on 16S rRNA gene amplicons data analysis and which different advantages and disadvantages each one offers.

So I'll try to use the three ones that you mentioned above: QIIME, MOTHUR and Usearch.

But there is many problems to reach my goal. One of them is the different database used and another one is the different OTU picking methods, e.g. de novo, closed-reference and open-reference.

Anyway I'll try.

Again, thank you, António