↓ Skip to main content

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

Overview of attention for article published in Nature Biotechnology, January 2018
Altmetric Badge

About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • One of the highest-scoring outputs from this source (#7 of 7,017)
  • 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

dimensions_citation
591 Dimensions

Readers on

mendeley
1438 Mendeley
citeulike
5 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 2,476 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 1,438 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 <1%
Unknown 1437 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 327 23%
Researcher 268 19%
Student > Master 189 13%
Student > Bachelor 178 12%
Other 62 4%
Other 225 16%
Unknown 189 13%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 497 35%
Agricultural and Biological Sciences 363 25%
Computer Science 74 5%
Engineering 54 4%
Medicine and Dentistry 50 3%
Other 164 11%
Unknown 236 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 1502. 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 31 March 2020.
All research outputs
#2,512
of 15,388,227 outputs
Outputs from Nature Biotechnology
#7
of 7,017 outputs
Outputs of similar age
#100
of 366,745 outputs
Outputs of similar age from Nature Biotechnology
#2
of 75 outputs
Altmetric has tracked 15,388,227 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 7,017 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 31.2. 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 366,745 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.