Can qiime2 be used for the PacBio SMRT full-length 16S rRNA sequencing data?

Hi everyone,
When I ues a 16s full-length sequence in qiime2 for analysis,there are some problems in step “Sequence quality control and feature table construction”. As shown below:
DADA2 R package version: 1.6.0

Filtering …
Learning Error Rates
Initializing error rates to maximum possible estimate.
Error in dada_uniques(names(derep[[i]]$uniques), unname(derep[[i]]$uniques), :
Input sequences exceed the maximum allowed string length.
Calls: dada -> dada_uniques -> .Call
My concerns boil down to two questions:
I haven’t been able to find any information regarding whether qiime2 is suitable for use on PacBio SMRT Cell data. Does qiime2 not apply to the PacBio SMRT Cell data?
Thanks,
jin

Hi Jin,
Right now DADA2 is not suitable for using with long-read data like Pac Bio. You should be able to use an OTU method instead.

I’ve been seeing more and more interest in Pac Bio CCR amplicons though, so it’s definitely something on our radar now for the future.

2 Likes

Thanks for your attention, I am looking forward to the new plugin for long-read data!

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