Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

Research output: Contribution to journalJournal articleResearchpeer-review

Standard

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. / Frøslev, Tobias Guldberg; Kjøller, Rasmus; Bruun, Hans Henrik; Ejrnæs, Rasmus; Brunbjerg, Ane Kirstine; Pietroni, Carlotta; Hansen, Anders Johannes.

In: Nature Communications, Vol. 8, No. 1, 1188, 30.10.2017.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Frøslev, TG, Kjøller, R, Bruun, HH, Ejrnæs, R, Brunbjerg, AK, Pietroni, C & Hansen, AJ 2017, 'Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates', Nature Communications, vol. 8, no. 1, 1188. https://doi.org/10.1038/s41467-017-01312-x

APA

Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications, 8(1), [1188]. https://doi.org/10.1038/s41467-017-01312-x

Vancouver

Frøslev TG, Kjøller R, Bruun HH, Ejrnæs R, Brunbjerg AK, Pietroni C et al. Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications. 2017 Oct 30;8(1). 1188. https://doi.org/10.1038/s41467-017-01312-x

Author

Frøslev, Tobias Guldberg ; Kjøller, Rasmus ; Bruun, Hans Henrik ; Ejrnæs, Rasmus ; Brunbjerg, Ane Kirstine ; Pietroni, Carlotta ; Hansen, Anders Johannes. / Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. In: Nature Communications. 2017 ; Vol. 8, No. 1.

Bibtex

@article{e904659cf0084942a3570eb2f42b2265,
title = "Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates",
abstract = "DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation.",
author = "Fr{\o}slev, {Tobias Guldberg} and Rasmus Kj{\o}ller and Bruun, {Hans Henrik} and Rasmus Ejrn{\ae}s and Brunbjerg, {Ane Kirstine} and Carlotta Pietroni and Hansen, {Anders Johannes}",
year = "2017",
month = "10",
day = "30",
doi = "10.1038/s41467-017-01312-x",
language = "English",
volume = "8",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "nature publishing group",
number = "1",

}

RIS

TY - JOUR

T1 - Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

AU - Frøslev, Tobias Guldberg

AU - Kjøller, Rasmus

AU - Bruun, Hans Henrik

AU - Ejrnæs, Rasmus

AU - Brunbjerg, Ane Kirstine

AU - Pietroni, Carlotta

AU - Hansen, Anders Johannes

PY - 2017/10/30

Y1 - 2017/10/30

N2 - DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation.

AB - DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants paired with plant ITS2 metabarcoding data of DNA extracted from soil from 130 sites in Denmark spanning major environmental gradients. OTU tables are produced with several different OTU definition algorithms and subsequently curated with LULU, and validated against field survey data. LULU curation consistently improves α-diversity estimates and other biodiversity metrics, and does not require a sequence reference database; thus, it represents a promising method for reliable biodiversity estimation.

UR - http://www.scopus.com/inward/record.url?scp=85032577891&partnerID=8YFLogxK

U2 - 10.1038/s41467-017-01312-x

DO - 10.1038/s41467-017-01312-x

M3 - Journal article

VL - 8

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 1188

ER -

ID: 185402299