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Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

Overview of attention for article published in BMC Microbiology, June 2015
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (78th percentile)

Mentioned by

twitter
8 tweeters
patent
1 patent

Citations

dimensions_citation
121 Dimensions

Readers on

mendeley
231 Mendeley
citeulike
1 CiteULike
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Title
Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis
Published in
BMC Microbiology, June 2015
DOI 10.1186/s12866-015-0450-4
Pubmed ID
Authors

Liyou Wu, Chongqing Wen, Yujia Qin, Huaqun Yin, Qichao Tu, Joy D. Van Nostrand, Tong Yuan, Menting Yuan, Ye Deng, Jizhong Zhou

Abstract

Although high-throughput sequencing, such as Illumina-based technologies (e.g. MiSeq), has revolutionized microbial ecology, adaptation of amplicon sequencing for environmental microbial community analysis is challenging due to the problem of low base diversity. A new phasing amplicon sequencing approach (PAS) was developed by shifting sequencing phases among different community samples from both directions via adding various numbers of bases (0-7) as spacers to both forward and reverse primers. Our results first indicated that the PAS method substantially ameliorated the problem of unbalanced base composition. Second, the PAS method substantially improved the sequence read base quality (an average of 10 % higher of bases above Q30). Third, the PAS method effectively increased raw sequence throughput (~15 % more raw reads). In addition, the PAS method significantly increased effective reads (9-47 %) and the effective read sequence length (16-96 more bases) after quality trim at Q30 with window 5. In addition, the PAS method reduced half of the sequencing errors (0.54-1.1 % less). Finally, two-step PCR amplification of the PAS method effectively ameliorated the amplification biases introduced by the long barcoded PCR primers. The developed strategy is robust for 16S rRNA gene amplicon sequencing. In addition, a similar strategy could also be used for sequencing other genes important to ecosystem functional processes.

Twitter Demographics

The data shown below were collected from the profiles of 8 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 231 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 1%
Portugal 2 <1%
United Kingdom 2 <1%
Belgium 1 <1%
Netherlands 1 <1%
Canada 1 <1%
Estonia 1 <1%
Spain 1 <1%
Mexico 1 <1%
Other 0 0%
Unknown 218 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 52 23%
Student > Ph. D. Student 46 20%
Student > Master 40 17%
Student > Bachelor 21 9%
Student > Doctoral Student 15 6%
Other 32 14%
Unknown 25 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 101 44%
Biochemistry, Genetics and Molecular Biology 40 17%
Environmental Science 19 8%
Immunology and Microbiology 10 4%
Engineering 4 2%
Other 24 10%
Unknown 33 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 6. 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 05 June 2019.
All research outputs
#2,920,377
of 15,175,259 outputs
Outputs from BMC Microbiology
#330
of 2,281 outputs
Outputs of similar age
#49,732
of 233,449 outputs
Outputs of similar age from BMC Microbiology
#1
of 1 outputs
Altmetric has tracked 15,175,259 research outputs across all sources so far. Compared to these this one has done well and is in the 77th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,281 research outputs from this source. They receive a mean Attention Score of 3.9. This one has done well, scoring higher than 83% 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 233,449 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 78% 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