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LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

Overview of attention for article published in Giga Science, August 2015
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (95th percentile)

Mentioned by

blogs
2 blogs
twitter
38 tweeters
peer_reviews
1 peer review site
facebook
1 Facebook page
googleplus
1 Google+ user

Citations

dimensions_citation
68 Dimensions

Readers on

mendeley
158 Mendeley
citeulike
1 CiteULike
Title
LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads
Published in
Giga Science, August 2015
DOI 10.1186/s13742-015-0076-3
Pubmed ID
Authors

René L. Warren, Chen Yang, Benjamin P. Vandervalk, Bahar Behsaz, Albert Lagman, Steven J. M. Jones, Inanç Birol

Abstract

Owing to the complexity of the assembly problem, we do not yet have complete genome sequences. The difficulty in assembling reads into finished genomes is exacerbated by sequence repeats and the inability of short reads to capture sufficient genomic information to resolve those problematic regions. In this regard, established and emerging long read technologies show great promise, but their current associated higher error rates typically require computational base correction and/or additional bioinformatics pre-processing before they can be of value. We present LINKS, the Long Interval Nucleotide K-mer Scaffolder algorithm, a method that makes use of the sequence properties of nanopore sequence data and other error-containing sequence data, to scaffold high-quality genome assemblies, without the need for read alignment or base correction. Here, we show how the contiguity of an ABySS Escherichia coli K-12 genome assembly can be increased greater than five-fold by the use of beta-released Oxford Nanopore Technologies Ltd. long reads and how LINKS leverages long-range information in Saccharomyces cerevisiae W303 nanopore reads to yield assemblies whose resulting contiguity and correctness are on par with or better than that of competing applications. We also present the re-scaffolding of the colossal white spruce (Picea glauca) draft assembly (PG29, 20 Gbp) and demonstrate how LINKS scales to larger genomes. This study highlights the present utility of nanopore reads for genome scaffolding in spite of their current limitations, which are expected to diminish as the nanopore sequencing technology advances. We expect LINKS to have broad utility in harnessing the potential of long reads in connecting high-quality sequences of small and large genome assembly drafts.

Twitter Demographics

The data shown below were collected from the profiles of 38 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 158 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 1%
Canada 2 1%
Sweden 2 1%
Brazil 2 1%
Korea, Republic of 1 <1%
Norway 1 <1%
France 1 <1%
Netherlands 1 <1%
Argentina 1 <1%
Other 3 2%
Unknown 142 90%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 41 26%
Researcher 40 25%
Student > Master 24 15%
Student > Doctoral Student 11 7%
Student > Bachelor 11 7%
Other 23 15%
Unknown 8 5%
Readers by discipline Count As %
Agricultural and Biological Sciences 81 51%
Biochemistry, Genetics and Molecular Biology 37 23%
Computer Science 21 13%
Engineering 4 3%
Immunology and Microbiology 1 <1%
Other 4 3%
Unknown 10 6%

Attention Score in Context

This research output has an Altmetric Attention Score of 34. 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 05 July 2018.
All research outputs
#544,075
of 14,155,547 outputs
Outputs from Giga Science
#134
of 664 outputs
Outputs of similar age
#11,639
of 235,560 outputs
Outputs of similar age from Giga Science
#1
of 1 outputs
Altmetric has tracked 14,155,547 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 96th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 664 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 23.8. This one has done well, scoring higher than 79% 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 235,560 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 95% 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