Ten simple rules for implementing deep amplicon sequencing in parasitology

Deep amplicon sequencing is transforming parasitology by enabling high-throughput profiling of parasite communities and detection of resistance-associated genetic variants. Despite its growing adoption, many researchers face challenges in implementation, and its full potential is often hindered by challenges in experimental design, including marker selection, data analysis and reproducibility. This article presents ten simple rules for applying deep amplicon sequencing in parasitology, developed through expert consensus at a deep amplicon sequencing symposium during the 2025 World Association for the Advancement of Veterinary Parasitology conference. These rules cover essential aspects from formulating research questions and choosing appropriate markers to managing data workflows and contributing to reference databases. We highlight the importance of integrating deep amplicon sequencing with traditional parasitological methods, ensuring transparent reporting and investing in capacity building. Whether you are new to deep amplicon sequencing or seeking to improve your current practices, these guidelines offer practical advice to enhance the robustness, reproducibility, and impact of your research. By adopting these principles, parasitologists can contribute to, and advance, a more reliable and collaborative scientific landscape.

Authors

Institutions

Publication Details

Journal
International Journal for Parasitology
Published
2025-11-01
DOI
https://doi.org/10.1016/j.ijpara.2025.11.003
Citations
1
Primary Topic
Helminth infection and control
Type
article
Field-Weighted Citation Impact
2.35
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Ten simple rules for implementing deep amplicon sequencing in parasitology

Lucas Christian de Sousa‐Paula, Khalid M. Mohammedsalih, María Martínez Valladares, Barbora Pafčo et al.
1 citations
International Journal for Parasitology
Helminth infection and control
2.35
article

Ten simple rules for implementing deep amplicon sequencing in parasitology

Lucas Christian de Sousa‐Paula, Khalid M. Mohammedsalih, María Martínez Valladares, Barbora Pafčo, Stephen R. Doyle, Laura Maté, Ana Cláudia Alexandre de Albuquerque, Candela Cantón, Lynsey Melville, Richard A. Jones, Mohamed Helal, Lucas G. Huggins, Osama Zahid, Abdul Jabbar, Emily Kate Francis, Juan Pedro Lirón, Amanda McEvoy, John S. Gilleard, Jan R Šlapeta, César Cristiano Bassetto, Pablo Godoy, Vito Colella, Abdul Ghafar, Mike Evans, Alicia Rojas, Grace Mulcahy, Lívio Martins Costa, Martin K. Nielsen, Alex Chambers, Laura Peachey, David J. Bartley, Joby Robleto-Quesada, Benedict Karani, Orla Byrne, Naoki Hayashi
article en
1 citations

Abstract

Deep amplicon sequencing is transforming parasitology by enabling high-throughput profiling of parasite communities and detection of resistance-associated genetic variants. Despite its growing adoption, many researchers face challenges in implementation, and its full potential is often hindered by challenges in experimental design, including marker selection, data analysis and reproducibility. This article presents ten simple rules for applying deep amplicon sequencing in parasitology, developed through expert consensus at a deep amplicon sequencing symposium during the 2025 World Association for the Advancement of Veterinary Parasitology conference. These rules cover essential aspects from formulating research questions and choosing appropriate markers to managing data workflows and contributing to reference databases. We highlight the importance of integrating deep amplicon sequencing with traditional parasitological methods, ensuring transparent reporting and investing in capacity building. Whether you are new to deep amplicon sequencing or seeking to improve your current practices, these guidelines offer practical advice to enhance the robustness, reproducibility, and impact of your research. By adopting these principles, parasitologists can contribute to, and advance, a more reliable and collaborative scientific landscape.

International Journal for Parasitology
University College Dublin (IE), Ain Shams University (EG), The University of Sydney (AU), National Development and Research Institutes (US), Roslin Institute (GB), Teagasc - The Irish Agriculture and Food Development Authority (IE), Cairo University (EG), Aberystwyth University (GB), The University of Melbourne (AU), University of Calgary (CA), Aarhus University (DK), Hokkaido University (JP), Wellcome Sanger Institute (GB), Universidad de Costa Rica (CR), University of Bristol (GB), AgResearch (NZ), Centro Científico Tecnológico - Tandil (AR), Roslin Cells (United Kingdom) (GB), National Institute of Allergy and Infectious Diseases (US), Moredun Research Institute (GB), Sydney Institute of Marine Science (AU), Czech Academy of Sciences, Institute of Vertebrate Biology (CZ), AgriBio (AU), Animal Health Research Institute (TW), Instituto de Ganadería de Montaña (ES), Universidade Federal do Maranhão (BR), Université de Montréal (CA), Freie Universität Berlin (DE), University of Glasgow (GB), Universidade Estadual Paulista (Unesp) (BR), Universidad de León (ES)
Openalex Percentile: Top 9%
Helminth infection and control
2.35
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.