VirGA - Virus Genome Assembly

VirGA is a collection of scripts and dependencies that work together to autonomously construct semi de novo large DNA virus genomes. It can begin with raw next generation sequencing (NGS) reads and concludes with a fully annotated and evaluated genome assembly. Please thoroughly read VirGA’s documentation and contact us with any questions you may have: moriah@psu.edu

Contents:

• Introduction
• Installation
  • Installation Methods
  • Linux Installation
  • Virtual Machine (VM) Installation
• Usage
  • Running VirGA
  • Overview of VirGA Output
  • STEP_1–Preprocessing Output
  • STEP_2–Multi_SSAKE_Assembly Output
  • STEP_3–Linerarize_and_Annotate Output
  • STEP_4–Assembly_Assessment Output
  • VirGA_Report Output
• Examples
  • Test case #1: HSV1 assembly using 250,000 paired-end reads
  • Test case #2: Adding wet-bench corrections to assembled genome
• Contact, Citing
  • Contact
  • Citing