| Title |
CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline
|
|---|---|
| Published in |
BMC Genomics, April 2017
|
| DOI | 10.1186/s12864-017-3717-3 |
| Pubmed ID | |
| Authors |
Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar, W. Florian Fricke |
| Abstract |
The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise. |
X Demographics
The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 3 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 2 | 67% |
| Members of the public | 1 | 33% |
Mendeley readers
The data shown below were compiled from readership statistics for 59 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 59 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 12 | 20% |
| Student > Master | 11 | 19% |
| Student > Ph. D. Student | 8 | 14% |
| Student > Bachelor | 6 | 10% |
| Student > Doctoral Student | 2 | 3% |
| Other | 9 | 15% |
| Unknown | 11 | 19% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 14 | 24% |
| Agricultural and Biological Sciences | 12 | 20% |
| Computer Science | 9 | 15% |
| Immunology and Microbiology | 3 | 5% |
| Engineering | 3 | 5% |
| Other | 7 | 12% |
| Unknown | 11 | 19% |
Attention Score in Context
This research output has an Altmetric Attention Score of 3. 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 30 April 2017.
All research outputs
#14,340,301
of 24,960,237 outputs
Outputs from BMC Genomics
#4,866
of 11,123 outputs
Outputs of similar age
#154,475
of 315,239 outputs
Outputs of similar age from BMC Genomics
#94
of 227 outputs
Altmetric has tracked 24,960,237 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 11,123 research outputs from this source. They receive a mean Attention Score of 4.8. This one has gotten more attention than average, scoring higher than 54% of its peers.
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We're also able to compare this research output to 227 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 56% of its contemporaries.