QIIME2 Nanopore 18S full length Amplicon sequenced data analysis

General Discussion
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1

Hello everyone,
I am new to 18S rRNA data analysis, I Have used qiime2 for illumina 16S rRNA, but now I want to run the analysis for Nanopore 18S full length Amplicon sequencing data.
I am unable to find a solid straight forward workflow/pipeline for the same. I want to use both PR2 and SILVA 138.2 databases as taxonomy classifier. I have tried MetONTIIME but due to docker/singularity issue unable to use it.

Please help me on this issue. please suggest pipeline/Workflow that can work for 18S rRNA full length data.

Thank you.

3

Hi @Adyasha_Panda, Welcome to the :qiime2: Forum!

I've asked the moderators to see if anyone knows of a good reference for doing this with QIIME 2. We'll try to follow up with some guidance.

4

Hi, Thank you.
I would really appreciate if there is any reference for analysis full length 18S amplicon sequenced data from Nanopore using qiime2. I have classified the taxonomy database. I am going to use PR2 database for this purpose.

Thank you

5

Hi @Adyasha_Panda,
18S amplicon studies are not my speciality but my understanding is the workflow is generally very similar to the 16s data. What specifically is not working for you about SILVA 138.2 databases as taxonomy classifier?

Here are so resources from the forum:

https://forum.qiime2.org/t/18s-data-taxonomic-classifiers/17964/10

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