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A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

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    0576721 - MBÚ 2025 GB eng J - Journal Article
    Hakimzadeh, A. - Abdala Asbun, A. - Albanese, D. - Bernard, M. - Buchner, D. - Callahan, B. - Caporaso, J. G. - Curd, E. - Djemiel, C. - Brandstrom Durling, M. - Elbrecht, V. - Gold, Z. - Gweon, H. S. - Hajibabaei, M. - Hildebrand, F. - Mikryukov, V. - Normandeau, E. - Ozkurt, E. - M. Palmer, J. - Pascal, G. - Porter, T. M. - Straub, D. - Vasar, M. - Větrovský, Tomáš - Zafeiropoulos, H. - Anslan, S.
    A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.
    Molecular Ecology Resources. (2023). ISSN 1755-098X. E-ISSN 1755-0998
    R&D Projects: GA ČR(CZ) GA21-17749S
    Institutional support: RVO:61388971
    Keywords : amplicon data analysis * bioinformatics * environmental DNA * metabarcoding * pipeline * review
    OECD category: Microbiology
    Impact factor: 7.7, year: 2022
    Method of publishing: Open access
    https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13847

    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.
    Permanent Link: https://hdl.handle.net/11104/0346151

     
     
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