Does Qiime2 support Pacbio for the time being?

Eman · March 22, 2021, 5:32pm

Hello,

I am wondering if Qiime2 does support the analysis of Pacbio generated sequences?

Thanks

colinbrislawn · March 23, 2021, 1:09am

Hello Eman,

As of today, the q2-dada2 QIIME 2 plugin does not support long reads, but folks are working on it!

github.com/qiime2/q2-dada2

Add long-read support

opened 09:17PM - 20 Sep 18 UTC

closed 08:50PM - 15 Nov 22 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).

DADA2 itself does support Pacbio reads, as shown in this tutorial, so one options is to process data using DADA2, then import those into QIIME 2 for downstream analysis.

I hope this helps!

Eman · March 23, 2021, 6:00am

Hello Colin,

So, the only way, for the time being, is to use DADA2 in R, however, I do not know why they process each replicate separately in the tutorial. I hope Qiime releases the new plugins concerning Pacbio technology very soon. Qiime people make our life much easier!

Many thanks!
Eman

system · April 23, 2021, 12:00pm

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