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.
2 answers
ONT offers a rRNA workflow: https://github.com/epi2me-labs/wf-16s
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
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you can build your custom one using nfcore modules