# taxonomical asignment questions: SILVA, PR2 and vsearch vs BLAST

**URL:** https://forum.qiime2.org/t/taxonomical-asignment-questions-silva-pr2-and-vsearch-vs-blast/18675
**Category:** User Support
**Tags:** taxonomy
**Created:** [February 27, 2021, 12:52pm UTC](https://forum.qiime2.org/t/taxonomical-asignment-questions-silva-pr2-and-vsearch-vs-blast/18675 "2021-02-27T12:52:55Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [March 1, 2021, 4:08pm UTC](https://forum.qiime2.org/t/taxonomical-asignment-questions-silva-pr2-and-vsearch-vs-blast/18675/2 "2021-03-01T16:08:00Z")

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> [@SaraGajas](#):
>
> Is there any way I can choose using only 16S references?

You can simply use RESCRIPt to make a 16S-rRNA gene reference set from the SILVA db. This is the tool we currently use to generate the SILVA files on the data resources page.

> [@Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt](https://forum.qiime2.org/t/processing-filtering-and-evaluating-the-silva-database-and-other-reference-sequence-data-with-rescript/15494):
>
> construction Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt [RESCRIPt](https://github.com/bokulich-lab/RESCRIPt) (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for construc…

I often prefer to keep the 18S rRNA genes as there can be amplified off-targets. Leaving these 18S sequences in the reference set as "decoys" helps with identifying non-16S rRNA gene sequences. However, it can be beneficial to make a SILVA 16S rRNA only reference db to help limit memory usage. So, following the above linked tutorial and only keep `Bacteria` and `Archaea` should do the trick.

> [@SaraGajas](#):
>
> re there any resources available for PR2 to use with BLAST classification on Qiime2 like the SILVA reference sequences and associated taxonomy files ?

Not currently, although other users may have made their own. Hopefully, others will check into this thread. Otherwise, you can also download [16S rRNA gene files from GTDB](https://data.gtdb.ecogenomic.org/releases/) and re-format them for import into QIIME 2. Obviously you should be able to do the same for [PR2](https://pr2-database.org/).

> [@SaraGajas](#):
>
> I’ve tried them both with a set of 12 samples and while the process with vsearch lasted ~ 38h, with BLAST it took just 1 hour. Is this explained by the fact that in vsearch global alignments are made while in vsearch they are local?

What parameter settings did you use for vsearch and blast?

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