Guidance

DISCLAIMER: The identification methods used and the data summarized are for public health surveillance or investigational purposes only and must NOT be communicated to the patient, their care provider, or placed in the patient’s medical record. These results should NOT be used for diagnosis, treatment, or assessment of individual patient health or management.

• Home
• Dependencies and Install
  • Quick Start
  • All The Details
    • Install Nextflow
    • Configuring Nextflow
    • Installing Container Software
    • Download Database Files for Kraken2
  • Run PHoeNIx
  • Testing Install
• Running PHoeNIx
  • Input Parameters
  • Input: --mode PHOENIX or CDC_PHOENIX
  • Input: --mode SCAFFOLDS or CDC_SCAFFOLDS
  • Input: --mode SRA or CDC_SRA
  • Input: --mode COMBINE_GRIPHINS
  • Input: --mode UPDATE_PHOENIX
  • Outputs
    • File Structure
    • Output File Overview
• Pipeline Overview
  • QC
  • Analysis of Trimmed Reads
  • Analysis Using Trimmed Reads
  • Assembly
  • QC of Assembled Scaffolds
  • Analysis of Assembled Scaffolds >= 500bps
  • Pipeline QC Checks
  • Understanding Griphin Summary
    • AR Gene Reporting
    • MLST Allele Symbols
  • Visualizing PHoeNIx Output
    • RShiny App
    • MultiQC
• Documentation for Databases
  • Standard Databases
  • Species-specific Databases
• Running PHoeNIx on Different Systems
  • Adjusting Memory/CPU Usage
  • Configuration for Running PHoeNIx on a HPC
  • Running PHoeNIx with the STaPH-B Toolkit
  • Running PHoeNIx >=2.1.0 on ICA
  • Running PHoeNIx <=v1.1.1 on Terra
  • Running PHoeNIx >=v2.0.0 on Terra
  • Summarizing PHoeNIx Output >=v2.2.0 on Terra
• Versioning Control and Reproducibility
• Troubleshooting
• Guidance
• Contributing and Issues
  • Requesting Changes
• Beta Testing