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Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes.

ABSTRACT: Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of data. Identification of operational taxonomic units (OTUs) is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogeny-based. The number of identified sequences in the reference databases affects the precision of identification. This paper compares the identification of marine nematode OTUs using alignment-based, tree-based and phylogeny-based approaches. Because the nematode reference dataset is limited in its taxonomic scope, OTUs can only be assigned to higher taxonomic categories, families. The phylogeny-based approach using the evolutionary placement algorithm provided the largest number of positively assigned OTUs and was least affected by erroneous sequences and limitations of reference data, compared to alignment-based and tree-based approaches.

SUBMITTER: Holovachov O

PROVIDER: S-EPMC5579096 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes.

Holovachov Oleksandr O Haenel Quiterie Q Bourlat Sarah J SJ Jondelius Ulf U

Royal Society open science 20170816 8

Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of data. Identification of operational taxonomic units (OTUs) is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogeny-based. The number of identified sequences in the reference databases affects the precision of identification. This paper compares the iden ...[more]

PMID: 28878981

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Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes.

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Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes.

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