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Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data

Overview of attention for article published in Genome Medicine, 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)
  • Average Attention Score compared to outputs of the same age and source

Mentioned by

twitter
12 tweeters

Citations

dimensions_citation
36 Dimensions

Readers on

mendeley
87 Mendeley
Summary Twitter Dimensions citations
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Title
Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data
Published in
Genome Medicine, June 2015
DOI 10.1186/s13073-015-0176-9
Pubmed ID
26136847
Authors

Jason W. Sahl, James M. Schupp, David A. Rasko, Rebecca E. Colman, Jeffrey T. Foster, Paul Keim

Abstract

We describe an approach for genotyping bacterial strains from low coverage genome datasets, including metagenomic data from complex samples. Sequence reads from unknown samples are aligned to a reference genome where the allele states of known SNPs are determined. The Whole Genome Focused Array SNP Typing (WG-FAST) pipeline can identify unknown strains with much less read data than is needed for genome assembly. To test WG-FAST, we resampled SNPs from real samples to understand the relationship between low coverage metagenomic data and accurate phylogenetic placement. WG-FAST can be downloaded from https://github.com/jasonsahl/wgfast.

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Twitter Demographics

The data shown below were collected from the profiles of 12 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 87 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 3%
Portugal 1 1%
Sweden 1 1%
Brazil 1 1%
Russia 1 1%
Denmark 1 1%
Unknown 79 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 25 29%
Researcher 16 18%
Student > Bachelor 11 13%
Student > Doctoral Student 7 8%
Student > Master 7 8%
Other 10 11%
Unknown 11 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 32 37%
Biochemistry, Genetics and Molecular Biology 19 22%
Computer Science 9 10%
Medicine and Dentistry 4 5%
Engineering 3 3%
Other 8 9%
Unknown 12 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 7. 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 04 January 2016.
All research outputs
#4,562,727
of 23,342,232 outputs
Outputs from Genome Medicine
#867
of 1,458 outputs
Outputs of similar age
#56,999
of 267,596 outputs
Outputs of similar age from Genome Medicine
#23
of 34 outputs
Altmetric has tracked 23,342,232 research outputs across all sources so far. Compared to these this one has done well and is in the 80th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,458 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 25.8. This one is in the 40th percentile – i.e., 40% of its peers scored the same or lower than it.
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 267,596 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 34 others from the same source and published within six weeks on either side of this one. This one is in the 32nd percentile – i.e., 32% of its contemporaries scored the same or lower than it.

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