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Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values

Overview of attention for article published in BMC Medical Genomics, August 2016
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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 (81st percentile)
  • High Attention Score compared to outputs of the same age and source (82nd percentile)

Mentioned by

blogs
1 blog
twitter
4 tweeters

Citations

dimensions_citation
7 Dimensions

Readers on

mendeley
23 Mendeley
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Title
Fast comparison of genomic and meta-genomic reads with alignment-free measures based on quality values
Published in
BMC Medical Genomics, August 2016
DOI 10.1186/s12920-016-0193-6
Pubmed ID
Authors

Matteo Comin, Michele Schimd

Abstract

Sequencing technologies are generating enormous amounts of read data, however assembly of genomes and metagenomes remain among the most challenging tasks. In this paper we study the comparison of genomes and metagenomes only based on read data, using word counts statistics called alignment-free thus not requiring reference genomes or assemblies. Quality scores produced by sequencing platforms are fundamental for various analyses, moreover future-generation sequencing platforms, will produce longer reads but with error rate around 15 %. In this context it will be fundamental to exploit quality values information within the framework of alignment-free measures. In this paper we present a family of alignment-free measures, called d (q) -type, that are based on k-mer counts and quality values. These statistics can be used to compare genomes and metagenomes based on their read sets. Results show that the evolutionary relationship of genomes can be reconstructed based on the direct comparison of theirs reads sets. The use of quality values on average improves the classification accuracy, and its contribution increases when the reads are more noisy. Also the comparison of metagenomic microbial communities can be performed efficiently. Similar metagenomes are quickly detected, just by processing their read data, without the need of costly alignments.

Twitter Demographics

The data shown below were collected from the profiles of 4 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 23 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 2 9%
Spain 1 4%
Unknown 20 87%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 39%
Researcher 7 30%
Professor > Associate Professor 2 9%
Student > Master 2 9%
Professor 1 4%
Other 1 4%
Unknown 1 4%
Readers by discipline Count As %
Computer Science 11 48%
Agricultural and Biological Sciences 5 22%
Biochemistry, Genetics and Molecular Biology 5 22%
Environmental Science 1 4%
Unknown 1 4%

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 27 October 2017.
All research outputs
#1,605,407
of 12,059,719 outputs
Outputs from BMC Medical Genomics
#91
of 558 outputs
Outputs of similar age
#44,371
of 239,101 outputs
Outputs of similar age from BMC Medical Genomics
#5
of 28 outputs
Altmetric has tracked 12,059,719 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 558 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.1. This one has done well, scoring higher than 83% 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 239,101 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 81% of its contemporaries.
We're also able to compare this research output to 28 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 82% of its contemporaries.