Can QIIME2 be used to analysis the PacBio SMRT full-length 16S rRNA sequencing data?

MengZhang · November 26, 2019, 3:41pm

Hello everyone,
I wanna to known, if the QIIME2 supports to analysis the sequencing data by Pac-Bio Single Molecule Real-Time Sequencing Technique.
I attended this can’t be supported before, How about now.
Hope your reply,
Thanks.

colinbrislawn · November 26, 2019, 11:06pm

Hello MengZhang,

Welcome to the forums!

Thank you for looking as past posts about PacBio, and asking about the current status.
Dada2 does support PacBio reads right now, and I asked the developer about when this is coming to Qiime 2. Looks like Qiime 2 still does not support long reads, see:

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.

Let me know if you have more questions!

Colin

MengZhang · November 29, 2019, 12:51am

Hello Colin,
Thanks for your attention, thanks you help me ask this question on Github.
I don’t have more question!
Meng

system · December 30, 2019, 7:02am

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