Welcome to iVirus’s documentation!

iVirus is “a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets.” We’re focused on 3 major areas:

1. Provide easy-to-use tools/apps through CyVerse and now KBase! (wahoo!)
2. Detailed protocols through Protocols.io.
3. Databases and collections of “useful” viral datasets to the broader research community on CyVerse and KBase.

We won’t go into much detail on the “science” side of iVirus - for that - check the references below and the those associated with specific tools.

This site is mainly to provide a singular resource for the code and links to use and/or understand the tools. If you’re here and don’t want coding stuff but want to be able to run the tools you find on CyVerse, then…

Go here for a collection of iVirus related protocols.

Go here was the original location for iVirus. It’s not code-heavy, and was designed while iVirus (and its sister site, iMicrobe) was in its infancy. Over the years iVirus has grown onto multiple platforms, each with its own documentation requirements, and users - from non-informatician scientists to full-blown CS programmers - want info at the level of their appropriate backgrounds. Unfortunately, there’s no single-page solution (or maybe there is, contact me if you are aware of one) to integrating all iVirus tools, documentation, historical background, among others. Sadly, there’s only so many websites (nearly a dozen DIFFERENT PLACES) one can manage simultaneously and keep up-to-date, and iVirus.us has fallen a bit out of date. While we try to keep it updated, it’s usually the last place. So look to this site for the most recent information, alongside protocols.io.

Contents:

• Introduction and Overview
  • Full Disclosure on App Selection
  • Authorship and Citations
• Apps and Tools
  • The Basics: Using Singularity
  • Quality Control Apps
  • Gene Calling
  • Assemblers
  • Annotations, Sequence Analysis
  • Viral Analysis
  • In some stage of development
• Protocols
  • Guides and Use Cases
  • Processing a Viral Metagenome
  • Mapping Metagenomic Reads to a Reference Collection
• Singularity 101
  • Singularity Notes
  • Before you begin
  • Typical Workflow
  • Create Singularity definition file
  • Build Singularity image with the definitions file
  • Bugs?
  • Links
• Building-A-Pipeline
  • From Containers to Pipelines
  • Before you begin
  • Step 1 - On your local machine
  • Step 2 - In the docker container
  • Step 3 - On your local machine
  • Step 4 - On TACC

References:

• iVirus: Facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. (2017) Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B.L., and Sullivan, M.B. ISME Journal

Funding:

We’d be remiss if we didn’t mention the support of awards that make iVirus possible. iVirus wouldn’t be possible without the following grants: Gordon and Betty Moore Foundation Investigator Award (#3790), and since Sept 2018 an NSF Advances in Biological Infrastructure Award (#1759874).

The NSF award page is here

Thanks so much for making this work possible!

Indices and tables

• Index
• Module Index
• Search Page