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Updated: Jul 28, 2026

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
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.
Summary:
NanoASV is a conda environment and snakemake-based workflow using state-of-the-art bioinformatics software to process full-length SSU rRNA (16S/18S) amplicons acquired with Oxford Nanopore Sequencing technology. Its strength lies in reproducibility, portability, and the possibility to run offline, allowing in-field analysis. It can be installed on the Nanopore MK1C sequencing device and process data locally.
Availability And Implementation:
Source code and documentation are freely available at https://github.com/ImagoXV/NanoASV and Zenodo archive at https://doi.org/10.5281/zenodo.14730742.

