↓ Skip to main content

Linked read technology for assembling large complex and polyploid genomes

Overview of attention for article published in BMC Genomics, September 2018
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (90th percentile)
  • High Attention Score compared to outputs of the same age and source (96th percentile)

Mentioned by

blogs
1 blog
twitter
20 X users
wikipedia
1 Wikipedia page

Citations

dimensions_citation
32 Dimensions

Readers on

mendeley
82 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
Linked read technology for assembling large complex and polyploid genomes
Published in
BMC Genomics, September 2018
DOI 10.1186/s12864-018-5040-z
Pubmed ID
Authors

Alina Ott, James C. Schnable, Cheng-Ting Yeh, Linjiang Wu, Chao Liu, Heng-Cheng Hu, Clifton L. Dalgard, Soumik Sarkar, Patrick S. Schnable

Abstract

Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly. Here we describe a de novo maize B73 genome assembly generated via linked read technology which contains ~ 172,000 scaffolds with an N50 of 89 kb that cover 50% of the genome. Based on comparisons to the B73 reference genome, 91% of linked read contigs are accurately assembled. Because it was possible to identify errors with > 76% accuracy using machine learning, it may be possible to identify and potentially correct systematic errors. Complex polyploids represent one of the last grand challenges in genome assembly. Linked read technology was able to successfully resolve the two subgenomes of the recent allopolyploid, proso millet (Panicum miliaceum). Our assembly covers ~ 83% of the 1 Gb genome and consists of 30,819 scaffolds with an N50 of 912 kb. Our analysis provides a framework for future de novo genome assemblies using linked reads, and we suggest computational strategies that if implemented have the potential to further improve linked read assemblies, particularly for repetitive genomes.

X Demographics

X Demographics

The data shown below were collected from the profiles of 20 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 82 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 82 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 17 21%
Student > Ph. D. Student 10 12%
Student > Master 7 9%
Student > Bachelor 6 7%
Student > Doctoral Student 5 6%
Other 9 11%
Unknown 28 34%
Readers by discipline Count As %
Agricultural and Biological Sciences 20 24%
Biochemistry, Genetics and Molecular Biology 18 22%
Computer Science 5 6%
Medicine and Dentistry 2 2%
Psychology 1 1%
Other 2 2%
Unknown 34 41%
Attention Score in Context

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 03 December 2023.
All research outputs
#1,641,376
of 24,929,945 outputs
Outputs from BMC Genomics
#332
of 11,111 outputs
Outputs of similar age
#33,875
of 340,767 outputs
Outputs of similar age from BMC Genomics
#8
of 188 outputs
Altmetric has tracked 24,929,945 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 11,111 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done particularly well, scoring higher than 97% 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 340,767 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 90% of its contemporaries.
We're also able to compare this research output to 188 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 96% of its contemporaries.