Is the dada2 plugin version installed in qiime 2019.1 suitable for PacBio 16S rRNA analysis?

ja.morillo · April 10, 2019, 11:11am

Dear colleagues:
I need to analyze full length rRNA 16S sequences obtained from a PacBio machine. In order to check if I can do do it with qiime2 and get ASVs (instead of OTUs), I have check the version of the dada2 package installed within the dada2 plugin (last version of qiime2 available, 2019.1). Apparently the version of dada2 that we have is 1.6.0 (please see shell output below).
In the oficial web of dada2, they announce that it is posible to process dada2 reads after their last version, dada2 1.10 (https://benjjneb.github.io/dada2/index.html).
Sorry for the trivial question, but all this means that currently it is not possible to analize dada2 reads with qiime2-dada2, right? I am a bit confused becasue there are some threads in the qiime2 forum disscussing how to analyze PacBio reads within qiime2.
In case that the above were true, is it posible to use Deblur for PacBio? Any benckmarking analysis/pipeline is available for PacBio in qiime2?
Last question -just to understand things better-, is there any technical reason to dont update the dada2 plugin with the last version of the dada2 package available?
Thanks for all qiime2 and plugins developers and community for your immense contribution!

checking packages in qiime2 2019.1

(qiime2-2019.1) qiime2@qiime2core2019-1:~$ conda list

packages in environment at /home/qiime2/miniconda/envs/qiime2-2019.1:

Name Version Build Channel

q2-dada2 2019.1.0 py36_0 qiime2/label/r2019.1
bioconductor-dada2 1.6.0 r3.4.1_0 bioconda

colinbrislawn · April 10, 2019, 5:55pm

Hello Jose,

Great question. Good detective work about dada2 1.10 integration in Qiime.

According to this issue, this is planned for the Q2 dada plugin by the end of 2019.

github.com/qiime2/q2-dada2

Add long-read support

opened 09:17PM - 20 Sep 18 UTC

benjjneb

**Improvement Description** Add long-read support **Current Behavior** We'v…e added support for PacBio long-read amplicon sequencing to the devel version of the R package and it seems to work quite well. Preprint: High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. **Proposed Behavior** I think it will make sense to add this as a tech-specific ```denoise-pacbio``` command in the plugin. This is similar to the ```denoise-pyro``` approach already in the plugin, with the purpose of having a dedicated command being to automatically turn on the right flags and options for PacBio data rather than relying on the user to do so. There is a downside in the repetition of much of the code between the different ```denoise-[technology]``` commands. **References** 1. Preprint: [High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution](https://www.biorxiv.org/content/early/2018/08/15/392332).

Until then, you bet is to do the analysis directly in R by following the dada2 1.10 tutorial.

Colin

ja.morillo · April 11, 2019, 8:12am

Hello Colin,

OK I will try in R, then. Pity, because qiime makes things easier! But DADA2 web/support is also excellent.
Thanks a lot,
Jose

system · May 12, 2019, 2:12pm

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