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Large-scale contamination of microbial isolate genomes by Illumina PhiX control

Overview of attention for article published in Standards in Genomic Sciences, March 2015
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • One of the highest-scoring outputs from this source (#4 of 565)
  • High Attention Score compared to outputs of the same age (92nd percentile)

Citations

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203 Mendeley
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Title
Large-scale contamination of microbial isolate genomes by Illumina PhiX control
Published in
Standards in Genomic Sciences, March 2015
DOI 10.1186/1944-3277-10-18
Pubmed ID
Authors

Supratim Mukherjee, Marcel Huntemann, Natalia Ivanova, Nikos C Kyrpides, Amrita Pati

Abstract

With the rapid growth and development of sequencing technologies, genomes have become the new go-to for exploring solutions to some of the world's biggest challenges such as searching for alternative energy sources and exploration of genomic dark matter. However, progress in sequencing has been accompanied by its share of errors that can occur during template or library preparation, sequencing, imaging or data analysis. In this study we screened over 18,000 publicly available microbial isolate genome sequences in the Integrated Microbial Genomes database and identified more than 1000 genomes that are contaminated with PhiX, a control frequently used during Illumina sequencing runs. Approximately 10% of these genomes have been published in literature and 129 contaminated genomes were sequenced under the Human Microbiome Project. Raw sequence reads are prone to contamination from various sources and are usually eliminated during downstream quality control steps. Detection of PhiX contaminated genomes indicates a lapse in either the application or effectiveness of proper quality control measures. The presence of PhiX contamination in several publicly available isolate genomes can result in additional errors when such data are used in comparative genomics analyses. Such contamination of public databases have far-reaching consequences in the form of erroneous data interpretation and analyses, and necessitates better measures to proofread raw sequences before releasing them to the broader scientific community.

Twitter Demographics

The data shown below were collected from the profiles of 13 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 203 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 5 2%
United Kingdom 3 1%
Germany 1 <1%
South Africa 1 <1%
Brazil 1 <1%
Italy 1 <1%
New Zealand 1 <1%
Ukraine 1 <1%
Korea, Republic of 1 <1%
Other 1 <1%
Unknown 187 92%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 47 23%
Researcher 39 19%
Student > Master 33 16%
Student > Bachelor 20 10%
Student > Doctoral Student 11 5%
Other 29 14%
Unknown 24 12%
Readers by discipline Count As %
Agricultural and Biological Sciences 71 35%
Biochemistry, Genetics and Molecular Biology 59 29%
Immunology and Microbiology 9 4%
Medicine and Dentistry 7 3%
Computer Science 6 3%
Other 23 11%
Unknown 28 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 22. 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 09 February 2022.
All research outputs
#1,301,710
of 21,131,454 outputs
Outputs from Standards in Genomic Sciences
#4
of 565 outputs
Outputs of similar age
#18,615
of 248,195 outputs
Outputs of similar age from Standards in Genomic Sciences
#1
of 1 outputs
Altmetric has tracked 21,131,454 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 565 research outputs from this source. They receive a mean Attention Score of 2.6. This one has done particularly well, scoring higher than 99% 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 248,195 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 92% 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