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Protocols

EukRef specifications

Information


Unique identifier OMICS_32178
Name EukRef
Alternative name Eukaryotic Reference Database
Restrictions to use None
Community driven Yes
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Javier del Campo

Publication for Eukaryotic Reference Database

EukRef citations

 (3)
library_books

Haptophyte Diversity and Vertical Distribution Explored by 18S and 28S Ribosomal RNA Gene Metabarcoding and Scanning Electron Microscopy

2017
PMCID: 5574017
PMID: 27973742
DOI: 10.1111/jeu.12388

[…] Phylogenies were performed following EUKREF RAxML‐EPA (Evolutionary Placement Algorithm) pipeline (del Campo, pers. commun.) for a more reliable taxonomic assignation of reads than by BLAST. Curated haptophyte 18S and 28S rRNA gene refer […]

call_split

Metabarcoding based fungal diversity on coarse and fine particulate organic matter in a first order stream in Nova Scotia, Canada

2016
F1000Res
PMCID: 4755416
PMID: 26918122
DOI: 10.5256/f1000research.7930.r12182
call_split See protocol

[…] ting procedure ( http://www.mothur.org/wiki/Schloss_SOP, accessed 7/2012), implementing denoising, trimming, alignment, filtering, chimera removal, classification, and preclustering steps against the eukaryotic reference database provided by Mothur. OTUs were calculated on a 97% basis of a final alignment with a median length of 279 nt and statistics (diversity estimates and similarities) were don […]

library_books

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system

2013
eLife
PMCID: 3796315
PMID: 24137541
DOI: 10.7554/eLife.01104.016

[…] s into a tree of the Silva 108 eukaryotic representative set using the maximum likelihood EPA algorithm within RAxML (). Taxonomy was assigned to de novo reads using RDP () retrained on the Silva 108 eukaryotic reference database at the genus level within QIIME. […]

Citations

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EukRef institution(s)
Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CSIC, Barcelona, Spain; Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Departments of Marine Sciences & Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA; Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, Roscoff, France; Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada; Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA; Department of Zoology, University of British Columbia, Vancouver, BC, Canada
EukRef funding source(s)
Supported by the Gordon and Betty Moore Foundation and the National Science Foundation.

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