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Autor
Abdala Asbun, Alejandro 1 Albanese, Davide 1 Anslan, Sten 1 Bernard, Maria 1 Brandström Durling, Mikael 1 Buchner, Dominik 1 Callahan, Benjamin 1 Caporaso, J Gregory 1 Curd, Emily 1 Djemiel, Christophe 1 Elbrecht, Vasco 1 Gold, Zachary 1 Gweon, Hyun S 1 Hajibabaei, Mehrdad 1 Hakimzadeh, Ali 1 Hildebrand, Falk 1 M Palmer, Jonathan 1 Mikryukov, Vladimir 1 Normandeau, Eric 1 Pascal, Géraldine 1
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Pracoviště
Agroécologie INRAE Institut Agro Univ... 1 Aquatic Ecosystem Research University... 1 Center for Applied Microbiome Science... 1 Center for Forest Mycology Research N... 1 Department of Biological and Environm... 1 Department of Forest Mycology and Pla... 1 Department of Integrative Biology and... 1 Department of Marine Microbiology and... 1 Department of Population Health and P... 1 Earlham Institute Norwich Research Pa... 1 GenPhySE Université de Toulouse INRAE... 1 Gut Microbes and Health Quadram Insti... 1 INRAE AgroParisTech GABI Université P... 1 INRAE SIGENAE Jouy en Josas France 1 Institut de Biologie Intégrative et d... 1 Institute of Ecology and Earth Scienc... 1 KU Leuven Department of Microbiology ... 1 Laboratory of Environmental Microbiol... 1 Quantitative Biology Center Universit... 1 School of Biological Sciences Univers... 1
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Autor
Abdala Asbun, Alejandro 1 Albanese, Davide 1 Anslan, Sten 1 Bernard, Maria 1 Brandström Durling, Mikael 1 Buchner, Dominik 1 Callahan, Benjamin 1 Caporaso, J Gregory 1 Curd, Emily 1 Djemiel, Christophe 1 Elbrecht, Vasco 1 Gold, Zachary 1 Gweon, Hyun S 1 Hajibabaei, Mehrdad 1 Hakimzadeh, Ali 1 Hildebrand, Falk 1 M Palmer, Jonathan 1 Mikryukov, Vladimir 1 Normandeau, Eric 1 Pascal, Géraldine 1
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Pracoviště
Agroécologie INRAE Institut Agro Univ... 1 Aquatic Ecosystem Research University... 1 Center for Applied Microbiome Science... 1 Center for Forest Mycology Research N... 1 Department of Biological and Environm... 1 Department of Forest Mycology and Pla... 1 Department of Integrative Biology and... 1 Department of Marine Microbiology and... 1 Department of Population Health and P... 1 Earlham Institute Norwich Research Pa... 1 GenPhySE Université de Toulouse INRAE... 1 Gut Microbes and Health Quadram Insti... 1 INRAE AgroParisTech GABI Université P... 1 INRAE SIGENAE Jouy en Josas France 1 Institut de Biologie Intégrative et d... 1 Institute of Ecology and Earth Scienc... 1 KU Leuven Department of Microbiology ... 1 Laboratory of Environmental Microbiol... 1 Quantitative Biology Center Universit... 1 School of Biological Sciences Univers... 1
- Publikační typ
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- Nejvíce citované
PubMed
37548515
PubMed Central
PMC10847385
DOI
10.1111/1755-0998.13847
Knihovny.cz E-zdroje
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.
- Klíčová slova
- amplicon data analysis, bioinformatics, environmental DNA, metabarcoding, pipeline, review,
- MeSH
- analýza dat MeSH
- Archaea genetika klasifikace MeSH
- Bacteria genetika klasifikace MeSH
- environmentální DNA genetika MeSH
- Eukaryota genetika klasifikace MeSH
- metagenomika metody MeSH
- software * MeSH
- taxonomické DNA čárové kódování * metody MeSH
- výpočetní biologie * metody MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- environmentální DNA MeSH
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