Full length 18S rRNA data from Nanopre

Question

[Adyasha]

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.

[1769mkc]

you can build your custom one using nfcore modules

Answer 1

[GenoMax]

ONT offers a rRNA workflow: https://github.com/epi2me-labs/wf-16s

Answer 2

[Arthur]

Hey, we are currently developping a snakemake solution called NanoASV.

It works with personal reference dataset and/or SILVA 138.2

Please have a look and if you have any question, don't hesitate to open an issue

https://github.com/ImagoXV/NanoASV