UPARSE: highly accurate OTU sequences from microbial amplicon reads.

Affiliations

1. Independent Investigator, Tiburon, California, USA.
Authors
Edgar RC¹
(1 author)

Nature Methods, 18 Aug 2013, 10(10):996-998
https://doi.org/10.1038/nmeth.2604 PMID: 23955772

Abstract

Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.

Full text links

Read article at publisher's site: https://doi.org/10.1038/nmeth.2604

References

Articles referenced by this article (17)

Structure, function and diversity of the healthy human microbiome.
Human Microbiome Project Consortium, Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, FitzGerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, Martin JC, Mitreva M, Muzny DM, [...] White O
Nature, (7402):207-214 2012
MED: 22699609
Defining the core Arabidopsis thaliana root microbiome.
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL
Nature, (7409):86-90 2012
MED: 22859206
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG
Nat Methods, (1):57-59 2012
MED: 23202435
Accurate determination of microbial diversity from 454 pyrosequencing data.
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT
Nat Methods, (9):639-641 2009
MED: 19668203
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.
Reeder J, Knight R
Nat Methods, (9):668-669 2010
MED: 20805793
Removing noise from pyrosequenced amplicons.
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ
BMC Bioinformatics, 38 2011
MED: 21276213
UCHIME improves sensitivity and speed of chimera detection.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R
Bioinformatics, (16):2194-2200 2011
MED: 21700674
Ironing out the wrinkles in the rare biosphere through improved OTU clustering.
Huse SM, Welch DM, Morrison HG, Sogin ML
Environ Microbiol, (7):1889-1898 2010
MED: 20236171
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.
Schloss PD, Gevers D, Westcott SL
PLoS One, (12):e27310 2011
MED: 22194782
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, [...] Knight R
Nat Methods, (5):335-336 2010
MED: 20383131

Show 7 more references (10 of 17)

Citations & impact

Impact metrics

6,229

Citations

Jump to Citations

Data citations

Jump to Data

Citations of article over time

Alternative metrics

Altmetric item for https://www.altmetric.com/details/1697105

Altmetric
Discover the attention surrounding your research
https://www.altmetric.com/details/1697105

Article citations

The associations between gut microbiota and fecal metabolites with intelligence quotient in preschoolers.
Long J, Chen J, Huang H, Liang J, Pang L, Yang K, Wei H, Liao Q, Gu J, Zeng X, Huang D, Qiu X
BMC Microbiol, 24(1):431, 25 Oct 2024
Cited by: 0 articles | PMID: 39455934 | PMCID: PMC11515365
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring.
Mondal N, Dutta S, Chatterjee S, Sarkar J, Mondal M, Roy C, Chakraborty R, Ghosh W
PLoS One, 19(10):e0310595, 25 Oct 2024
Cited by: 0 articles | PMID: 39453910 | PMCID: PMC11508158
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
The intra-tumoral microbiome as a potential biomarker of response to external beam radiation therapy in cervical cancer.
Dou Z, Ai C, Zhang J, Li K, Jiang M, Wu X, Zhao C, Li Z, Zhang L
J Transl Med, 22(1):972, 28 Oct 2024
Cited by: 0 articles | PMID: 39468630 | PMCID: PMC11514760
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
Protorhabditis nematodes and pathogen-antagonistic bacteria interactively promote plant health.
Xu X, Jiang R, Wang X, Liu S, Dong M, Mao H, Li X, Ni Z, Lv N, Deng X, Xiong W, Tao C, Li R, Shen Q, Geisen S
Microbiome, 12(1):221, 28 Oct 2024
Cited by: 0 articles | PMID: 39468636 | PMCID: PMC11520073
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC
Microbial biomarker discovery in Parkinson's disease through a network-based approach.
Zhao Z, Chen J, Zhao D, Chen B, Wang Q, Li Y, Chen J, Bai C, Guo X, Hu N, Zhang B, Zhao R, Yuan J
NPJ Parkinsons Dis, 10(1):203, 26 Oct 2024
Cited by: 0 articles | PMID: 39461950 | PMCID: PMC11513973
This article is in the Europe PMC Open access subset. Refer to the copyright information in the article for licensing details.
Free full text in Europe PMC

Go to all (6,229) article citations

Other citations

Wikipedia

https://en.wikipedia.org/wiki/DNA_barcoding

Data

Data that cites the article

This data has been provided by curated databases and other sources that have cited the article.

Nucleotide sequences in ENA (3)

Sequence Read Archive(SRA)(ENA - SRP004306)
Sequence Read Archive(SRA)(ENA - SRP002443)
INSDC Project(ENA - PRJNA48465)

Search life-sciences literature (45,090,497 articles, preprints and more)

UPARSE: highly accurate OTU sequences from microbial amplicon reads.

Affiliations

Abstract

Full text links

References

Structure, function and diversity of the healthy human microbiome.

Defining the core Arabidopsis thaliana root microbiome.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Accurate determination of microbial diversity from 454 pyrosequencing data.

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.

Removing noise from pyrosequenced amplicons.

UCHIME improves sensitivity and speed of chimera detection.

Ironing out the wrinkles in the rare biosphere through improved OTU clustering.

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

QIIME allows analysis of high-throughput community sequencing data.

Citations & impact

Impact metrics

Citations of article over time

Alternative metrics

Article citations

The associations between gut microbiota and fecal metabolites with intelligence quotient in preschoolers.

Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring.

The intra-tumoral microbiome as a potential biomarker of response to external beam radiation therapy in cervical cancer.

Protorhabditis nematodes and pathogen-antagonistic bacteria interactively promote plant health.

Microbial biomarker discovery in Parkinson's disease through a network-based approach.

Other citations

Wikipedia

Data

Data that cites the article

Nucleotide sequences in ENA (3)

Similar Articles

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.

CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities.

MetAmp: combining amplicon data from multiple markers for OTU analysis.

rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing.

Partnerships & funding

Search life-sciences literature (45,090,497 articles, preprints and more)

UPARSE: highly accurate OTU sequences from microbial amplicon reads.

Author information

Affiliations

Abstract

Full text links

References

Citations & impact

Impact metrics

Citations of article over time

Alternative metrics

Article citations

Other citations

Wikipedia

Data

Data that cites the article

Nucleotide sequences in ENA (3)

Similar Articles

Partnerships & funding