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Title: Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.

Abstract

EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]; ; ; ; ;
  1. LANL
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
Contributing Org.:
Los Alamos National Laboratory (LANL)
OSTI Identifier:
1357891
Report Number(s):
EDGE; 005290WKSTN00
C17074
DOE Contract Number:
AC52-06NA25396
Resource Type:
Software
Software Revision:
00
Software Package Number:
005290
Software CPU:
WKSTN
Open Source:
Yes
Open Source under the GPL v3 License.
Source Code Available:
Yes
Related Software:
A series of open source bioinfomatics software. The list is documented in https://edge.readthedocs.io/en/develop/third_party.html.
Country of Publication:
United States

Citation Formats

Chain, Patrick, Lo, Chien-Chi, Li, Po-E, Davenport, Karen, Xu, Yan, Ahmed, Sanaa, Senin, Pavel, Shakya, Migun, Bishop-Lilly, Kimberly A., Anderson, Joseph J., Voegtly, Logan J., Philipson, Casandra W., and Hamilton, Theron. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.. Computer software. https://www.osti.gov//servlets/purl/1357891. Vers. 00. USDOE. 18 May. 2017. Web.
Chain, Patrick, Lo, Chien-Chi, Li, Po-E, Davenport, Karen, Xu, Yan, Ahmed, Sanaa, Senin, Pavel, Shakya, Migun, Bishop-Lilly, Kimberly A., Anderson, Joseph J., Voegtly, Logan J., Philipson, Casandra W., & Hamilton, Theron. (2017, May 18). Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x. (Version 00) [Computer software]. https://www.osti.gov//servlets/purl/1357891.
Chain, Patrick, Lo, Chien-Chi, Li, Po-E, Davenport, Karen, Xu, Yan, Ahmed, Sanaa, Senin, Pavel, Shakya, Migun, Bishop-Lilly, Kimberly A., Anderson, Joseph J., Voegtly, Logan J., Philipson, Casandra W., and Hamilton, Theron. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x.. Computer software. Version 00. May 18, 2017. https://www.osti.gov//servlets/purl/1357891.
@misc{osti_1357891,
title = {Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform, Version 1.5 and 1.x., Version 00},
author = {Chain, Patrick and Lo, Chien-Chi and Li, Po-E and Davenport, Karen and Xu, Yan and Ahmed, Sanaa and Senin, Pavel and Shakya, Migun and Bishop-Lilly, Kimberly A. and Anderson, Joseph J. and Voegtly, Logan J. and Philipson, Casandra W. and Hamilton, Theron},
abstractNote = {EDGE bioinformatics was developed to help biologists process Next Generation Sequencing data (in the form of raw FASTQ files), even if they have little to no bioinformatics expertise. EDGE is a highly integrated and interactive web-based platform that is capable of running many of the standard analyses that biologists require for viral, bacterial/archaeal, and metagenomic samples. EDGE provides the following analytical workflows: quality trimming and host removal, assembly and annotation, comparisons against known references, taxonomy classification of reads and contigs, whole genome SNP-based phylogenetic analysis, and PCR analysis. EDGE provides an intuitive web-based interface for user input, allows users to visualize and interact with selected results (e.g. JBrowse genome browser), and generates a final detailed PDF report. Results in the form of tables, text files, graphic files, and PDFs can be downloaded. A user management system allows tracking of an individual’s EDGE runs, along with the ability to share, post publicly, delete, or archive their results.},
url = {https://www.osti.gov//servlets/purl/1357891},
doi = {},
year = {Thu May 18 00:00:00 EDT 2017},
month = {Thu May 18 00:00:00 EDT 2017},
note =
}

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