EDGE: Empowering the Development of Genomics Expertise

• 1. EDGE ABCs
  • 1.1. About EDGE Bioinformatics
  • 1.2. Bioinformatics overview
  • 1.3. Computational Environment
• 2. Introduction
  • 2.1. What is EDGE?
  • 2.2. Why create EDGE?
• 3. System requirements
  • 3.1. Hardware Requirements
  • 3.2. Ubuntu 18.04
  • 3.3. CentOS 7
• 4. Installation
  • 4.1. EDGE Installation
  • 4.2. Configure SELinux on CentOS
  • 4.3. EDGE Docker image
• 5. Graphic User Interface (GUI)
  • 5.1. User Login
  • 5.2. Upload Files
  • 5.3. Initiating an analysis job
  • 5.4. Choosing processes/analyses
  • 5.5. Submission of a job
  • 5.6. Checking the status of an analysis job
  • 5.7. Monitoring the Resource Usage
  • 5.8. Management of Jobs
  • 5.9. Project List Table
  • 5.10. Other Methods of Accessing EDGE
• 6. Command Line Interface (CLI)
  • 6.1. Configuration File
  • 6.2. Test Run
  • 6.3. Descriptions of each module
  • 6.4. Other command-line utility scripts
• 7. Output
  • 7.1. Example Output
• 8. Databases
  • 8.1. EDGE provided databases
  • 8.2. Building bwa index
  • 8.3. SNP database genomes
  • 8.4. Ebola Reference Genomes
• 9. Third Party Tools
  • 9.1. Assembly
  • 9.2. Annotation
  • 9.3. Alignment
  • 9.4. Taxonomy Classification
  • 9.5. Phylogeny
  • 9.6. Specialty Genes
  • 9.7. Metagenome
  • 9.8. Visualization and Graphic User Interface
  • 9.9. Utility
  • 9.10. Amplicon Analysis
  • 9.11. RNA-Seq Analysis
• 10. FAQs and Troubleshooting
  • 10.1. FAQs
  • 10.2. Troubleshooting
  • 10.3. Discussions / Bugs Reporting
• 11. Copyright
• 12. Contact Us and Citation
  • 12.1. Citation