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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
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NanoASV: a snakemake workflow for reproducible field-based Nanopore full-length 16S metabarcoding amplicon data
Arthur Cousson1, Frédéric Mahé2,3, Ulysse Guyet4
1Eco&Sols, University of Montpellier, IRD, INRAe, CIRAD, Inst Agro, Montpellier F-34060, France.
Bioinformatics (Oxford, England)
|March 20, 2025
Summary
NanoASV is a bioinformatics workflow for processing SSU rRNA gene sequences from Oxford Nanopore sequencing. This tool enables reproducible, offline, and in-field analysis of amplicon data directly on sequencing devices.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Accurate analysis of microbial communities relies on sequencing ribosomal RNA genes.
- Oxford Nanopore Sequencing offers portable, real-time data acquisition.
- Existing workflows may lack portability or offline capabilities for field use.
Purpose of the Study:
- To develop a robust bioinformatics workflow for processing full-length SSU rRNA amplicons.
- To enable reproducible and portable analysis of amplicon sequencing data.
- To facilitate offline and in-field analysis using Oxford Nanopore Sequencing technology.
Main Methods:
- Developed NanoASV, a conda environment and snakemake-based workflow.
- Integrated state-of-the-art bioinformatics software for amplicon processing.
- Designed for compatibility with Oxford Nanopore Sequencing data.
Main Results:
- NanoASV processes full-length SSU rRNA (16S/18S) amplicons.
- The workflow ensures reproducibility and portability.
- Offline and in-field analysis is achievable.
Conclusions:
- NanoASV provides a powerful solution for processing nanopore-based amplicon sequencing data.
- The workflow can be installed and run locally on devices like the Nanopore MK1C.
- This facilitates immediate data analysis in diverse field settings.
