Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that...

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Bibliographic Details
Published in:Nucleic acids research Vol. 45; no. 1; pp. 67 - 80
Main Authors: Li, Po-E, Lo, Chien-Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., Chain, Patrick S.G.
Format: Journal Article
Language:English
Published: England Oxford University Press 09.01.2017
Subjects:
Anthrax - microbiology
Bacillus anthracis - classification
Bacillus anthracis - genetics
BASIC BIOLOGICAL SCIENCES
Biological Science
cloud compatible bioinformatics pipelines and workflows
Computational Biology - methods
Computer Science
Data Resources and Analyses
Ebolavirus - classification
Ebolavirus - genetics
Escherichia coli - classification
Escherichia coli - genetics
Escherichia coli Infections - microbiology
Hemorrhagic Fever, Ebola - virology
High-Throughput Nucleotide Sequencing
Humans
integrated web-based genome analysis
Internet
isolate and metagenome NGS data analysis and visualization
MATHEMATICS AND COMPUTING
next generation sequencing genomics and metagenome
Phylogeny
Plague - microbiology
Software
Yersinia pestis - classification
Yersinia pestis - genetics
ISSN:0305-1048, 1362-4962, 1362-4962
Online Access:Get full text
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Summary:Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.
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USDOE
AC52-06NA25396
LA-UR-15-27035; LA-UR-15-22467
USDOD
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkw1027