A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses
2024
Hakimzadeh, Ali | Abdala Asbun, Alejandro | Albanese, Davide | Bernard, Maria | Buchner, Dominik | Callahan, Benjamin | Caporaso, J. Gregory | Curd, Emily | Djemiel, Christophe | Brandström Durling, Mikael | Elbrecht, Vasco | Gold, Zachary | Gweon, Hyun | Hajibabaei, Mehrdad | Hildebrand, Falk | Mikryukov, Vladimir | Normandeau, Eric | Özkurt, Ezgi | M. Palmer, Jonathan | Pascal, Géraldine | Porter, Teresita | Straub, Daniel | Vasar, Martti | Větrovský, Tomáš | Zafeiropoulos, Haris | Anslan, Sten | Tartu University Hospital | Royal Netherlands Institute for Sea Research (NIOZ) | Athena Research and Innovation Centre (ARC) | Génétique Animale et Biologie Intégrative (GABI) ; AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Système d'Information des GENomes des Animaux d'Elevage (SIGENAE) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Universität Duisburg-Essen = University of Duisburg-Essen [Essen] | North Carolina State University [Raleigh] (NC State) ; University of North Carolina System (UNC) | Northern Arizona University [Flagstaff] | University of Vermont [Burlington] | Agroécologie [Dijon] ; Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) | Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet (SLU) | National Oceanic and Atmospheric Administration (NOAA) | University of Reading (UOR) | Centre for Ecology & Hydrology - Bush Estate ; Natural Environment Research Council (NERC) | University of Guelph [Guelf, Ontario, Canada] | Norwich Research Park ; The Genome Analysis Centre (TGAC) | Quadram Institute Bioscience [Norwich, U.K.] (QIB) ; Biotechnology and Biological Sciences Research Council (BBSRC) | Northern Research Station ; Forest Research | Génétique Physiologie et Systèmes d'Elevage (GenPhySE) ; Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | Eberhard Karls Universität Tübingen = University of Tübingen | Institute of Microbiology of the Czech Academy of Sciences [Prague, Czech Republic] (MBU / CAS) ; Czech Academy of Sciences [Prague] (CAS) | Rega Institute for Medical Research [Leuven] ; Catholic University of Leuven = Katholieke Universiteit Leuven (KU Leuven) | Deutsche Forschungsgemeinschaft (DFG), Grant/Award Number: EXC2124; European Regional Development Fund and the programme Mobilitas Pluss, Grant/Award Number: MOBTP198; Genome Canada and Ontario Genomics; Grantova Agentura Ceske Republiky, Grant/Award Number: 21-17749S; National Institute of General Medical Sciences, Grant/Award Number: P20GM103449
International audience
Afficher plus [+] Moins [-]anglais. 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 among 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‐two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.
Afficher plus [+] Moins [-]Mots clés AGROVOC
Informations bibliographiques
Cette notice bibliographique a été fournie par AgroParisTech
Découvrez la collection de ce fournisseur de données dans AGRIS