EDGE: Empowering the Development of Genomics Expertise

• 1. EDGE Introduction
  • 1.1. About EDGE Bioinformatics
  • 1.2. Bioinformatics overview
  • 1.3. Computational Environment
• 2. System requirements
  • 2.1. Hardware Requirements
  • 2.2. Ubuntu 14.04
  • 2.3. CentOS 7
• 3. Installation
  • 3.1. EDGE Installation
  • 3.2. EDGE Docker image
  • 3.3. EDGE VMware/OVF Image
• 4. Graphic User Interface (GUI)
  • 4.1. User Login
  • 4.2. Upload Files
  • 4.3. Initiating an analysis job
  • 4.4. Choosing processes/analyses
  • 4.5. Submission of a job
  • 4.6. Checking the status of an analysis job
  • 4.7. Monitoring the Resource Usage
  • 4.8. Management of Jobs
  • 4.9. Project List Table
  • 4.10. Other Methods of Accessing EDGE
• 5. Command Line Interface (CLI)
  • 5.1. Configuration File
  • 5.2. Test Run
  • 5.3. Descriptions of each module
  • 5.4. Other command-line utility scripts
• 6. Output
  • 6.1. Example Output
• 7. Databases
  • 7.1. EDGE provided databases
  • 7.2. Building bwa index
  • 7.3. SNP database genomes
  • 7.4. Ebola Reference Genomes
• 8. Third Party Tools
  • 8.1. Assembly
  • 8.2. Annotation
  • 8.3. Alignment
  • 8.4. Taxonomy Classification
  • 8.5. Phylogeny
  • 8.6. Specialty Genes
  • 8.7. Visualization and Graphic User Interface
  • 8.8. Utility
  • 8.9. Amplicon Analysis
• 9. Troubleshooting
  • 9.1. Coverage Issues
  • 9.2. Data Migration
  • 9.3. Known Issues
  • 9.4. Discussions / Bugs Reporting
• 10. Copyright
• 11. Contact Us and Citation
  • 11.1. Citation