Essential Site Maintenance: Authorea-powered sites will be updated circa 15:00-17:00 Eastern on Tuesday 5 November.
There should be no interruption to normal services, but please contact us at [email protected] in case you face any issues.

loading page

A pile of pipelines: an overview of the bioinformatics software for metabarcoding data analyses
  • +23
  • Ali Hakimzadeh,
  • Alejandro Abdala Asbun,
  • Davide Albanese,
  • Maria Bernard,
  • Dominik Buchner,
  • Benjamin Callahan,
  • Gregory Caporaso,
  • Emily Curd,
  • Christophe DJEMIEL,
  • Mikael Brandström Durling,
  • Vasco Elbrecht,
  • Zachary Gold,
  • Hyun Gweon,
  • Mehrdad Hajibabaei,
  • Falk Hildebrand,
  • Vladimir Mikryukov,
  • Eric Normandeau,
  • Ezgi Ozkurt,
  • Jonathan M. Palmer,
  • Géraldine Pascal,
  • Teresita Porter,
  • Daniel Straub,
  • Martti Vasar,
  • Tomáš Větrovský,
  • Haris Zafeiropoulos,
  • Sten Anslan
Ali Hakimzadeh
University of Tartu Institute of Ecology and Earth Sciences
Author Profile
Alejandro Abdala Asbun
NIOZ Royal Netherlands Institute for Sea Research
Author Profile
Davide Albanese
Fondazione Edmund Mach Istituto Agrario di San Michele all'Adige
Author Profile
Maria Bernard
Université Paris-Saclay
Author Profile
Dominik Buchner
University of Duisburg-Essen
Author Profile
Benjamin Callahan
North Carolina State University College of Veterinary Medicine
Author Profile
Gregory Caporaso
Northern Arizona University
Author Profile
Emily Curd
University of Vermont
Author Profile
Christophe DJEMIEL
INRA Dijon
Author Profile
Mikael Brandström Durling
Swedish University of Agricultural Sciences
Author Profile
Vasco Elbrecht
University of Duisburg-Essen
Author Profile
Zachary Gold
University of California San Diego
Author Profile
Hyun Gweon
Center for Ecology and Hydrology
Author Profile
Mehrdad Hajibabaei
University of Guelph
Author Profile
Falk Hildebrand
Quadram Institute Bioscience
Author Profile
Vladimir Mikryukov
University of Tartu Institute of Ecology and Earth Sciences
Author Profile
Eric Normandeau
Université Laval 'Institut de Biologie Intégrative et des Systèmes
Author Profile
Ezgi Ozkurt
Quadram Institute Bioscience
Author Profile
Jonathan M. Palmer
Northern Research Station, US Forest Service
Author Profile
Géraldine Pascal
GenPhySE
Author Profile
Teresita Porter
University of Guelph
Author Profile
Daniel Straub
University of Tübingen
Author Profile
Martti Vasar
University of Tartu Institute of Ecology and Earth Sciences
Author Profile
Tomáš Větrovský
Institute of Microbiology Czech Academy of Sciences
Author Profile
Haris Zafeiropoulos
KU Leuven Rega Institute for Medical Research
Author Profile
Sten Anslan
University of Tartu Institute of Ecology and Earth Sciences

Corresponding Author:[email protected]

Author Profile

Abstract

Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria, and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one amongst the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths, and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems, and particular attributes of thirty-one amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
09 Feb 2023Submitted to Molecular Ecology Resources
11 Feb 2023Submission Checks Completed
11 Feb 2023Assigned to Editor
11 Feb 2023Review(s) Completed, Editorial Evaluation Pending
10 Mar 2023Reviewer(s) Assigned
05 May 2023Editorial Decision: Revise Minor
02 Jun 20231st Revision Received
06 Jun 2023Submission Checks Completed
06 Jun 2023Assigned to Editor
06 Jun 2023Review(s) Completed, Editorial Evaluation Pending
06 Jul 2023Editorial Decision: Accept