Taxonomic classification question

Hello everyone! I´m about to perform the taxonomic classification of my 16S PE sequence data. The primers used for sequencing the V3-V4 region of my data were 341-F and 805-R. In qiime2 there is a trained classifier that is made for the 515-806 region, and the other is the full-length (both from the Greengenes database). The question is, is it ok to use the 515-806 classifier despite not being the same length extension of my primers (341-805)? or should I use the "full-length" version?
I decided to use Greengenes despite not being so curated as Silva, because in a previous publication I used Greengenes with qiime1. However, if the Silva database is much better, I will use it.
But I don´t know what taxonomic assignment method is the best in my case.

Apart from that, I made the denoisng step with the DADA2 denoising step and ASV were created, I do not have OTUs. So, is the Greengenes database an adequate db for this?
Thank you for your suggestions!


Hi @Vani_Maguire,

I would recommend using the full-length version if you do not have a set of reference files specifically curated for your amplicon region. Some users on the forum might have have made these files for you, just look around. :eyes:

Fortunately, we've made a plugin that will allow you to easily prepare your own SILVA classifier. :building_construction: Check out our awesome RESCRIPt plugin. You can follow the tutorial here to make your own classifier based on the 341-F and 805-R primers. :slight_smile:

Let us know if you run into any issues!


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Thank you very much Mike!!! I will try it!

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Hello! I am using RESCRIPt for taxonomy assignment of bacterial sequences, but is there any possibility of using the plugin with the UNITE database for fungal sequences? Thanks!

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Great question! We hope to add the ability to fetch reference data from UNITE and other databases. I can't comment on when that'll happen but it is on our "to do " list. :slight_smile:



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