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Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations

Overview of attention for article published in BMC Genomics, August 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • Good Attention Score compared to outputs of the same age (78th percentile)
  • High Attention Score compared to outputs of the same age and source (85th percentile)

Mentioned by

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18 tweeters

Citations

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15 Dimensions

Readers on

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61 Mendeley
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Title
Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations
Published in
BMC Genomics, August 2018
DOI 10.1186/s12864-018-4949-6
Pubmed ID
Authors

Timokratis Karamitros, Bonnie van Wilgenburg, Mark Wills, Paul Klenerman, Gkikas Magiorkinis

Abstract

Human cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCMV cultures but have also been observed in vivo. Thus, the assembly of HCMV whole genomes from technologies producing shorter than 500 bp sequences is technically challenging. Here we improved the reconstruction of HCMV full genomes by means of a hybrid, de novo genome-assembly bioinformatics pipeline upon data generated from the recently released MinION MkI B sequencer from Oxford Nanopore Technologies. The MinION run of the HCMV (strain TB40/E) library resulted in ~ 47,000 reads from a single R9 flowcell and in ~ 100× average read depth across the virus genome. We developed a novel, self-correcting bioinformatics algorithm to assemble the pooled HCMV genomes in three stages. In the first stage of the bioinformatics algorithm, long contigs (N50 = 21,892) of lower accuracy were reconstructed. In the second stage, short contigs (N50 = 5686) of higher accuracy were assembled, while in the final stage the high quality contigs served as template for the correction of the longer contigs resulting in a high-accuracy, full genome assembly (N50 = 41,056). We were able to reconstruct a single representative haplotype without employing any scaffolding steps. The majority (98.8%) of the genomic features from the reference strain were accurately annotated on this full genome construct. Our method also allowed the detection of multiple alternative sub-genomic fragments and non-canonical structures suggesting rearrangement events between the unique (UL /US) and the repeated (T/IRL/S) genomic regions. Third generation high-throughput sequencing technologies can accurately reconstruct full-length HCMV genomes including their low-complexity and highly repetitive regions. Full-length HCMV genomes could prove crucial in understanding the genetic determinants and viral evolution underpinning drug resistance, virulence and pathogenesis.

Twitter Demographics

The data shown below were collected from the profiles of 18 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 61 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 61 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 14 23%
Student > Master 10 16%
Student > Bachelor 9 15%
Student > Ph. D. Student 8 13%
Student > Doctoral Student 5 8%
Other 10 16%
Unknown 5 8%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 19 31%
Agricultural and Biological Sciences 13 21%
Immunology and Microbiology 8 13%
Computer Science 4 7%
Medicine and Dentistry 3 5%
Other 8 13%
Unknown 6 10%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. 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 18 September 2018.
All research outputs
#2,956,037
of 19,281,482 outputs
Outputs from BMC Genomics
#1,185
of 9,759 outputs
Outputs of similar age
#62,091
of 292,129 outputs
Outputs of similar age from BMC Genomics
#3
of 14 outputs
Altmetric has tracked 19,281,482 research outputs across all sources so far. Compared to these this one has done well and is in the 84th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 9,759 research outputs from this source. They receive a mean Attention Score of 4.5. This one has done well, scoring higher than 87% 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 292,129 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 14 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 85% of its contemporaries.