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

Software · Thu May 18 00:00:00 EDT 2017

OSTI ID:1357891

Chain, Patrick ^[1]; Lo, Chien-Chi ^[1]; Li, Po-E ^[1]; Davenport, Karen ^[1]; Xu, Yan ^[1]; Ahmed, Sanaa ^[1]; Senin, Pavel ^[1]; Shakya, Migun ^[1]; Bishop-Lilly, Kimberly A.; Anderson, Joseph J.; Voegtly, Logan J.; Philipson, Casandra W.; Hamilton, Theron

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1. LANL

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.

• Short Name / Acronym: EDGE; 005290WKSTN00
• Project Type: Open Source under the GPL v3 License.
• Site Accession Number: C17074
• Version: 00
• Programming Language(s): Medium: X; OS: Linux
• Research Organization: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: USDOE
• Contributing Organization: Los Alamos National Laboratory (LANL)
• DOE Contract Number: AC52-06NA25396
• OSTI ID: 1357891
• Country of Origin: United States