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X Demographics
Mendeley readers
Attention Score in Context
| Title |
PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly
|
|---|---|
| Published in |
BMC Bioinformatics, August 2018
|
| DOI | 10.1186/s12859-018-2307-y |
| Pubmed ID | |
| Authors |
Renato Renison Moreira Oliveira, Gisele Lopes Nunes, Talvâne Glauber Lopes de Lima, Guilherme Oliveira, Ronnie Alves |
| Abstract |
Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it's often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discovery and identification and have been widely used for taxonomic identification by targeting known gene regions that permit to discriminate these species. DNA barcode sequence analysis is usually carried out with processes and tools that still demand a high interaction with the user or researcher. To reduce at most such interaction, we proposed PIPEBAR, a pipeline for DNA chromatograms analysis of Sanger platform sequencing, ensuring high quality consensus sequences along with efficient running time. We also proposed a paired-end reads assembly tool, OverlapPER, which is used in sequence or independently of PIPEBAR. PIPEBAR is a command line tool to automatize the processing of large number of trace files. It is accurate as the proprietary Geneious tool and faster than most popular software for barcoding analysis. It is 7 times faster than Geneious and 14 times faster than SeqTrace for processing hundreds of barcoding sequences. OverlapPER is a novel tool for overlapping paired-end reads accurately that accepts both substitution and indel errors and returns both overlapped and non-overlapped regions between a pair of reads. OverlapPER obtained the best results compared to currently used tools when merging 1,000,000 simulated paired-end reads. PIPEBAR and OverlapPER run on most operating systems and are freely available, along with supporting code and documentation, at https://sourceforge.net/projects/PIPEBAR / and https://sourceforge.net/projects/overlapper-reads /. |
X Demographics
The data shown below were collected from the profiles of 5 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 Kingdom | 1 | 20% |
| Spain | 1 | 20% |
| Brazil | 1 | 20% |
| Unknown | 2 | 40% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 4 | 80% |
| Scientists | 1 | 20% |
Mendeley readers
The data shown below were compiled from readership statistics for 29 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 29 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Professor | 6 | 21% |
| Researcher | 6 | 21% |
| Student > Master | 3 | 10% |
| Student > Ph. D. Student | 3 | 10% |
| Student > Bachelor | 2 | 7% |
| Other | 4 | 14% |
| Unknown | 5 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 12 | 41% |
| Biochemistry, Genetics and Molecular Biology | 5 | 17% |
| Computer Science | 3 | 10% |
| Environmental Science | 1 | 3% |
| Engineering | 1 | 3% |
| Other | 0 | 0% |
| Unknown | 7 | 24% |
Attention Score in Context
This research output has an Altmetric Attention Score of 10. 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 24 August 2018.
All research outputs
#3,202,518
of 23,577,761 outputs
Outputs from BMC Bioinformatics
#1,116
of 7,418 outputs
Outputs of similar age
#64,523
of 332,229 outputs
Outputs of similar age from BMC Bioinformatics
#17
of 96 outputs
Altmetric has tracked 23,577,761 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 7,418 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one has done well, scoring higher than 84% 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 332,229 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 80% of its contemporaries.
We're also able to compare this research output to 96 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.