Welcome to WashU Virus Genome Browser’s documentation!

Contents:

• Navigating the WashU Virus Genome Browser
  • Virus Browser Home Page
  • Genomic Track View
    • Tracks
    • Apps
    • Settings
    • Help
  • Phylogenetic Tree View
    • Coloring Tree by Metadata
    • Identifying Strains of Interest
• SNV track
  • Understanding the SNV track
  • Density mode and the “zoomed-out” view
  • Full mode and the “zoomed-in” view
    • Nomenclature:
    • Color code:
  • Behind the SNV track: the “pairwise” format
    • Uploading interface
    • The pairwise format
    • To generate the pairwise format
    • Batch alignment from FASTA to pairwise format
    • Batch upload as json files
    • Upload json-formatted datahub
• SNV2 track
  • Functionality of SNV2 tracks
  • Defining the format of SNV2
  • Scripts for generating snv2 tracks
• Public Data Hubs
  • Loading in a public data hub
  • Introducing currently available public data hubs (As of May 24, 2020)
    • NCBI database
    • Nextstrain database
    • GISAID database
    • Diagnostics
    • Putative SARS-CoV-2 Immune Epitopes
    • Recombination Events
    • Viral RNA modifications
    • Viral RNA expression
    • SARS-CoV-2 host transcriptional responses database
• Contact Us
• Cite Us

Indices and tables

• Index
• Module Index
• Search Page