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

Hakimzadeh, A. ORCID: https://orcid.org/0000-0003-1336-7445, Abdala Asbun, A., Albanese, D., Bernard, M. ORCID: https://orcid.org/0000-0001-9005-5563, Buchner, D. ORCID: https://orcid.org/0000-0002-8499-5863, Callahan, B., Caporaso, J. G., Curd, E., Djemiel, C. ORCID: https://orcid.org/0000-0002-5659-7876, Brandström Durling, M. ORCID: https://orcid.org/0000-0001-6485-197X, Elbrecht, V. ORCID: https://orcid.org/0000-0003-4672-7099, Gold, Z., Gweon, S. ORCID: https://orcid.org/0000-0002-6218-6301, Hajibabaei, M. ORCID: https://orcid.org/0000-0002-8859-7977, Hildebrand, F., Mikryukov, V., Normandeau, E., Özkurt, E., M. Palmer, J., Pascal, G. ORCID: https://orcid.org/0000-0002-5250-6594, Porter, T. M., Straub, D., Vasar, M. ORCID: https://orcid.org/0000-0002-4674-932X, Větrovský, T., Zafeiropoulos, H. and Anslan, S. ORCID: https://orcid.org/0000-0002-2299-454X (2023) A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Molecular Ecology Resources. ISSN 1755-0998 doi: 10.1111/1755-0998.13847

Abstract/Summary

AbstractEnvironmental 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.

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/112961
Identification Number/DOI	10.1111/1755-0998.13847
Refereed	Yes
Divisions	Life Sciences > School of Biological Sciences > Department of Bio-Engineering
Publisher	Wiley
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