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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines
|
|---|---|
| Published in |
PLOS ONE, November 2012
|
| DOI | 10.1371/journal.pone.0049110 |
| Pubmed ID | |
| Authors |
Matthew Frampton, Richard Houlston |
| Abstract |
Pipelines for the analysis of Next-Generation Sequencing (NGS) data are generally composed of a set of different publicly available software, configured together in order to map short reads of a genome and call variants. The fidelity of pipelines is variable. We have developed ArtificialFastqGenerator, which takes a reference genome sequence as input and outputs artificial paired-end FASTQ files containing Phred quality scores. Since these artificial FASTQs are derived from the reference genome, it provides a gold-standard for read-alignment and variant-calling, thereby enabling the performance of any NGS pipeline to be evaluated. The user can customise DNA template/read length, the modelling of coverage based on GC content, whether to use real Phred base quality scores taken from existing FASTQ files, and whether to simulate sequencing errors. Detailed coverage and error summary statistics are outputted. Here we describe ArtificialFastqGenerator and illustrate its implementation in evaluating a typical bespoke NGS analysis pipeline under different experimental conditions. ArtificialFastqGenerator was released in January 2012. Source code, example files and binaries are freely available under the terms of the GNU General Public License v3.0. from https://sourceforge.net/projects/artfastqgen/. |
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.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 2 | 10% |
| France | 2 | 10% |
| Germany | 2 | 10% |
| Norway | 1 | 5% |
| Peru | 1 | 5% |
| Australia | 1 | 5% |
| Canada | 1 | 5% |
| United Kingdom | 1 | 5% |
| Montenegro | 1 | 5% |
| Other | 1 | 5% |
| Unknown | 7 | 35% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 12 | 60% |
| Scientists | 7 | 35% |
| Science communicators (journalists, bloggers, editors) | 1 | 5% |
Mendeley readers
The data shown below were compiled from readership statistics for 161 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 7 | 4% |
| United Kingdom | 2 | 1% |
| Spain | 2 | 1% |
| Switzerland | 1 | <1% |
| France | 1 | <1% |
| India | 1 | <1% |
| Germany | 1 | <1% |
| Colombia | 1 | <1% |
| Italy | 1 | <1% |
| Other | 0 | 0% |
| Unknown | 144 | 89% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 48 | 30% |
| Student > Ph. D. Student | 31 | 19% |
| Student > Master | 24 | 15% |
| Other | 10 | 6% |
| Student > Bachelor | 9 | 6% |
| Other | 27 | 17% |
| Unknown | 12 | 7% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 74 | 46% |
| Biochemistry, Genetics and Molecular Biology | 35 | 22% |
| Computer Science | 13 | 8% |
| Medicine and Dentistry | 7 | 4% |
| Immunology and Microbiology | 6 | 4% |
| Other | 11 | 7% |
| Unknown | 15 | 9% |
Attention Score in Context
This research output has an Altmetric Attention Score of 20. 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 11 July 2022.
All research outputs
#1,741,839
of 24,059,832 outputs
Outputs from PLOS ONE
#21,959
of 206,522 outputs
Outputs of similar age
#11,276
of 182,727 outputs
Outputs of similar age from PLOS ONE
#416
of 4,753 outputs
Altmetric has tracked 24,059,832 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 206,522 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 15.6. This one has done well, scoring higher than 89% 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 182,727 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 93% of its contemporaries.
We're also able to compare this research output to 4,753 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 91% of its contemporaries.