Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus-Reference-Cited by-同舟云学术

Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus

Published:2023-01-31 Issue:1 Volume:89 Page:
ISSN:0099-2240
Container-title:Applied and Environmental Microbiology
language:en
Short-container-title:Appl Environ Microbiol

Author:

Fitzpatrick Amy H.¹²³^ORCID,Rupnik Agnieszka²,O’Shea Helen³,Crispie Fiona¹,Keaveney Sinéad²^ORCID,Cotter Paul D.¹^ORCID

Affiliation:

1. Department of Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland

2. Department of Shellfish Microbiology, Marine Institute, Oranmore, Ireland

3. Department of Biological Sciences, Munster Technological University, Bishopstown, Ireland

Abstract

In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present. This study provides recommendations for the appropriate analysis and classification of norovirus amplicon HTS data and will be widely applicable during outbreak investigations.

Funder

Cullen Scholarship Programme

Publisher

American Society for Microbiology

Subject

Ecology,Applied Microbiology and Biotechnology,Food Science,Biotechnology

Link

https://journals.asm.org/doi/pdf/10.1128/aem.01522-22

Reference68 articles.

1. ICTV Virus Taxonomy Profile: Caliciviridae

2. Updated classification of norovirus genogroups and genotypes

3. Proposal for a unified norovirus nomenclature and genotyping