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Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

Overview of attention for article published in Microbiome, October 2014
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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 (90th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (60th percentile)

Mentioned by

twitter
24 tweeters
facebook
3 Facebook pages
googleplus
1 Google+ user

Citations

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45 Dimensions

Readers on

mendeley
229 Mendeley
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Title
Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation
Published in
Microbiome, October 2014
DOI 10.1186/2049-2618-2-39
Pubmed ID
Authors

Albi Celaj, Janet Markle, Jayne Danska, John Parkinson

Abstract

Microbiome-wide gene expression profiling through high-throughput RNA sequencing ('metatranscriptomics') offers a powerful means to functionally interrogate complex microbial communities. Key to successful exploitation of these datasets is the ability to confidently match relatively short sequence reads to known bacterial transcripts. In the absence of reference genomes, such annotation efforts may be enhanced by assembling reads into longer contiguous sequences ('contigs'), prior to database search strategies. Since reads from homologous transcripts may derive from several species, represented at different abundance levels, it is not clear how well current assembly pipelines perform for metatranscriptomic datasets. Here we evaluate the performance of four currently employed assemblers including de novo transcriptome assemblers - Trinity and Oases; the metagenomic assembler - Metavelvet; and the recently developed metatranscriptomic assembler IDBA-MT.

Twitter Demographics

The data shown below were collected from the profiles of 24 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 229 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 6 3%
Germany 2 <1%
Portugal 1 <1%
Chile 1 <1%
Australia 1 <1%
Brazil 1 <1%
Netherlands 1 <1%
Canada 1 <1%
Czechia 1 <1%
Other 2 <1%
Unknown 212 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 63 28%
Student > Ph. D. Student 62 27%
Student > Master 28 12%
Student > Bachelor 11 5%
Professor > Associate Professor 10 4%
Other 34 15%
Unknown 21 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 111 48%
Biochemistry, Genetics and Molecular Biology 39 17%
Environmental Science 19 8%
Computer Science 10 4%
Immunology and Microbiology 7 3%
Other 14 6%
Unknown 29 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 16. 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 01 December 2014.
All research outputs
#1,828,033
of 21,480,505 outputs
Outputs from Microbiome
#721
of 1,296 outputs
Outputs of similar age
#24,114
of 252,288 outputs
Outputs of similar age from Microbiome
#19
of 45 outputs
Altmetric has tracked 21,480,505 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 91st percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,296 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 40.7. This one is in the 44th percentile – i.e., 44% of its peers scored the same or lower than it.
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 252,288 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 45 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 60% of its contemporaries.