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Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

Overview of attention for article published in Giga Science, January 2016
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (94th percentile)

Mentioned by

blogs
2 blogs
policy
1 policy source
twitter
25 tweeters
peer_reviews
1 peer review site
facebook
1 Facebook page
googleplus
1 Google+ user

Citations

dimensions_citation
103 Dimensions

Readers on

mendeley
386 Mendeley
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Title
Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer
Published in
Giga Science, January 2016
DOI 10.1186/s13742-016-0111-z
Pubmed ID
Authors

Alfonso Benítez-Páez, Kevin J. Portune, Yolanda Sanz

Abstract

The miniaturised and portable DNA sequencer MinION™ has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinION™ system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences. Using R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. These data were sufficient to reconstruct more than 90 % of the 16S rRNA gene sequences for 20 different species present in a mock reference community. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to assign taxonomic classification down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using 'universal' primers. Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, the MinION™ DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements in nanopore chemistry, such as minimising base-calling errors and the nucleotide bias reported here for 16S amplicon sequencing, will further deliver more reliable information that is useful for the specific detection of microbial species and strains in complex ecosystems.

Twitter Demographics

The data shown below were collected from the profiles of 25 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 386 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 6 2%
United Kingdom 4 1%
Australia 2 <1%
India 1 <1%
Italy 1 <1%
Norway 1 <1%
Sweden 1 <1%
Bulgaria 1 <1%
Czechia 1 <1%
Other 7 2%
Unknown 361 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 111 29%
Student > Ph. D. Student 81 21%
Student > Master 50 13%
Student > Bachelor 25 6%
Professor > Associate Professor 19 5%
Other 66 17%
Unknown 34 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 159 41%
Biochemistry, Genetics and Molecular Biology 85 22%
Environmental Science 22 6%
Medicine and Dentistry 17 4%
Computer Science 16 4%
Other 40 10%
Unknown 47 12%

Attention Score in Context

This research output has an Altmetric Attention Score of 28. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 07 January 2020.
All research outputs
#720,581
of 15,383,358 outputs
Outputs from Giga Science
#176
of 740 outputs
Outputs of similar age
#19,674
of 342,904 outputs
Outputs of similar age from Giga Science
#1
of 1 outputs
Altmetric has tracked 15,383,358 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 95th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 740 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 23.3. This one has done well, scoring higher than 76% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 342,904 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 94% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them