Welcome to VirAmp’s documentation!

VirAmp is a galaxy-based system for fast virus genome assembly and variation discovery.

Quick Start Guide:

1. Launch the latest version of the “Szpara_Viramp” AMI from Amazon Web Services

2) SSH into the server and start the run.sh script using screen ./run.sh

Contents:

• Introduction
• Usage
  • One-click pipeline
  • Quality Control
  • Diginorm
  • de novo Contig assembly
  • Reference-based scaffolding
  • Reference-independent scaffolding
  • Gap closing
• Post-Assembly Analysis
  • QUAST REPORT
  • Assembly-Reference Alignment
  • Circos graph visualization
  • SNP analysis
  • Repeat and Tandem repeat analysis
• Custom installation of the VirAmp AMI
  • Step-1: Choosing the instance
  • Step-2: Review Instance type
  • Step-3: Launch the Instance
  • Step-4: Create Key-pairs
  • Log in to the new instance

• For further information on the individual tools VirAmp utilizes please see the following websites:

  • seqtk
  • diginorm
  • velvet
  • AMOS
  • Quast
  • MUMmer
  • Circos