EDGE
v1.5
  • 1. EDGE Introduction
  • 2. System requirements
  • 3. Installation
  • 4. Graphic User Interface (GUI)
  • 5. Command Line Interface (CLI)
  • 6. Output
  • 7. Databases
  • 8. Third Party Tools
  • 9. Troubleshooting
  • 10. Copyright
  • 11. Contact Us and Citation
EDGE
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  • EDGE: Empowering the Development of Genomics Expertise
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EDGE: Empowering the Development of Genomics ExpertiseΒΆ

  • 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
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© Copyright 2014-2017, EDGE Development Team Revision eb58878f.

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