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

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 S.; Hajibabaei, Mehrdad; Hildebrand, Falk; Mikryukov, Vladimir; Normandeau, Eric; Özkurt, Ezgi; M. Palmer, Jonathan; Pascal, Géraldine; Porter, Teresita M.; Straub, Daniel; Vasar, Martti; Větrovský, Tomáš; Zafeiropoulos, Haris; Anslan, Sten

doi:10.1111/1755-0998.13847

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The NOAA IR serves as an archival repository of NOAA-published products including scientific findings, journal articles, guidelines, recommendations, or other information authored or co-authored by NOAA or funded partners. As a repository, the NOAA IR retains documents in their original published format to ensure public access to scientific information.

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

2023
By Hakimzadeh, Ali ; Abdala Asbun, Alejandro ; Albanese, Davide ; ...
Source: Molecular Ecology Resources (2023)

[PDF-1.46 MB]

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Details:

Journal Title:

Molecular Ecology Resources
Personal Author:

Hakimzadeh, Ali ; Abdala Asbun, Alejandro ; Albanese, Davide ; Bernard, Maria ; Buchner, Dominik ; ... More +

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 S. ; Hajibabaei, Mehrdad ; Hildebrand, Falk ; Mikryukov, Vladimir ; Normandeau, Eric ; Özkurt, Ezgi ; M. Palmer, Jonathan ; Pascal, Géraldine ; Porter, Teresita M. ; Straub, Daniel ; Vasar, Martti ; Větrovský, Tomáš ; Zafeiropoulos, Haris ; Anslan, Sten Less -
NOAA Program & Office:

OAR (Oceanic and Atmospheric Research) ; PMEL (Pacific Marine Environmental Laboratory)

OAR (Oceanic and Atmospheric Research) ; PMEL (Pacific Marine Environmental Laboratory) Less -
Description:

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.
Keywords:

[+]

Biotechnology Ecology, Evolution, Behavior And Systematics Genetics
Source:

Molecular Ecology Resources (2023)
DOI:

https://doi.org/10.1111/1755-0998.13847
ISSN:

1755-098X;1755-0998;
Format:

PDF
Publisher:

Wiley
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Journal Article
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Accepted Manuscript
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Library
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urn:sha-512:16cb3fa8aaef4ec8daa14dc5d685bbf5a706a77faa714e0cdab79628a43ae650bf64da98f729f74484799bd35fae4af27d327e30f962d92581e90c4a3c89304a
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https://repository.library.noaa.gov/view/noaa/64073/noaa_64073_DS1.pdf
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