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Nanopore sequencing and assembly of a human genome with ultra-long reads

Overview of attention for article published in Nature Biotechnology, January 2018
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • One of the highest-scoring outputs from this source (#6 of 6,782)
  • High Attention Score compared to outputs of the same age (99th percentile)
  • High Attention Score compared to outputs of the same age and source (97th percentile)

Citations

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454 Dimensions

Readers on

mendeley
1289 Mendeley
citeulike
2 CiteULike
Title
Nanopore sequencing and assembly of a human genome with ultra-long reads
Published in
Nature Biotechnology, January 2018
DOI 10.1038/nbt.4060
Pubmed ID
Authors

Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Tom Nieto, Justin O'Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron R Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M Phillippy, Jared T Simpson, Nicholas J Loman, Matthew Loose

Abstract

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ∼3 Mb). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb). Incorporating an additional 5× coverage of these ultra-long reads more than doubled the assembly contiguity (NG50 ∼6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.

Twitter Demographics

The data shown below were collected from the profiles of 2,501 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 1,289 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 <1%
Unknown 1288 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 282 22%
Researcher 247 19%
Student > Master 164 13%
Student > Bachelor 161 12%
Other 60 5%
Other 230 18%
Unknown 145 11%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 438 34%
Agricultural and Biological Sciences 338 26%
Computer Science 72 6%
Engineering 48 4%
Medicine and Dentistry 46 4%
Other 158 12%
Unknown 189 15%

Attention Score in Context

This research output has an Altmetric Attention Score of 1524. 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 03 September 2019.
All research outputs
#1,735
of 14,204,167 outputs
Outputs from Nature Biotechnology
#6
of 6,782 outputs
Outputs of similar age
#92
of 358,949 outputs
Outputs of similar age from Nature Biotechnology
#2
of 75 outputs
Altmetric has tracked 14,204,167 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 99th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 6,782 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 28.5. 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 358,949 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 99% of its contemporaries.
We're also able to compare this research output to 75 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 97% of its contemporaries.