Full length 18S rRNA data from Nanopre
2
0
Entering edit mode
7 days ago
Adyasha • 0

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.

Linux • 394 views
ADD COMMENT
0
Entering edit mode

you can build your custom one using nfcore modules

ADD REPLY
1
Entering edit mode
7 days ago
GenoMax 147k

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

ADD COMMENT
1
Entering edit mode
7 days ago
Arthur ▴ 10

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

ADD COMMENT

Login before adding your answer.

Traffic: 2604 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6