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X Demographics
Mendeley readers
Attention Score in Context
| Title |
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
|
|---|---|
| Published in |
BMC Bioinformatics, December 2016
|
| DOI | 10.1186/s12859-016-1344-7 |
| Pubmed ID | |
| Authors |
Diego C. B. Mariano, Felipe L. Pereira, Edgar L. Aguiar, Letícia C. Oliveira, Leandro Benevides, Luís C. Guimarães, Edson L. Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique C. P. Figueiredo, Artur Silva, Rommel T. J. Ramos, Vasco A. C. Azevedo |
| Abstract |
The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net . |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 45 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 2% |
| Unknown | 44 | 98% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 9 | 20% |
| Student > Master | 8 | 18% |
| Student > Bachelor | 8 | 18% |
| Student > Ph. D. Student | 6 | 13% |
| Professor > Associate Professor | 3 | 7% |
| Other | 7 | 16% |
| Unknown | 4 | 9% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 10 | 22% |
| Computer Science | 8 | 18% |
| Biochemistry, Genetics and Molecular Biology | 7 | 16% |
| Engineering | 3 | 7% |
| Chemistry | 2 | 4% |
| Other | 6 | 13% |
| Unknown | 9 | 20% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. 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 28 July 2017.
All research outputs
#20,440,241
of 22,994,508 outputs
Outputs from BMC Bioinformatics
#6,886
of 7,311 outputs
Outputs of similar age
#355,854
of 421,626 outputs
Outputs of similar age from BMC Bioinformatics
#108
of 132 outputs
Altmetric has tracked 22,994,508 research outputs across all sources so far. This one is in the 1st percentile – i.e., 1% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,311 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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We're also able to compare this research output to 132 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.