Dataset Information

MetaPR² : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

ABSTRACT: In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recently as amplicon sequence variants (ASVs). This hampers comparative studies between different environments and data sets, for example examining the biogeographical patterns of specific groups/species, as well analysing the genetic microdiversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR² reference sequence database. This database, called metaPR² , contains 41 data sets corresponding to more than 4000 samples and 90,000 ASVs. The database, which is accessible through both a web-based interface (https://shiny.metapr2.org) and an R package, should prove very useful to all researchers working on protist diversity in a variety of systems.

SUBMITTER: Vaulot D

PROVIDER: S-EPMC9796713 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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metaPR<sup>2</sup> : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

Vaulot Daniel D Sim Clarence Wei Hung CWH Ong Denise D Teo Bryan B Biwer Charlie C Jamy Mahwash M Lopes Dos Santos Adriana A

Molecular ecology resources 20220713 8

In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities. The number of environmental data sets published has increased very rapidly. Although unprocessed sequence files are often publicly available, processed data, in particular clustered sequences, are rarely available in a usable format. Clustered sequences are reported as operational taxonomic units (OTUs) with different similarity levels or more recentl ...[more]

PMID: 35762265

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Dataset Information

MetaPR² : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

Publications

metaPR<sup>2</sup> : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

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Dataset Information

MetaPR2 : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

Publications

metaPR<sup>2</sup> : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

MetaPR² : A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.