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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F24%3A00576721" target="_blank" >RIV/61388971:_____/24:00576721 - isvavai.cz</a>
Result on the web
<a href="https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13847" target="_blank" >https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13847</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1111/1755-0998.13847" target="_blank" >10.1111/1755-0998.13847</a>

Result language
angličtina
Original language name
A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses
Original language 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.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10606 - Microbiology

Project
<a href="/en/project/GA21-17749S" target="_blank" >GA21-17749S: Economically important fungi and related organisms: distribution, diversity and human effects</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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