Learn about the iVirus project
iVirus started as a means to fill a void in the sequencing and analysis pipeline where few tools were designed with viruses in mind. Even today, many tools do not "think about" the unique challenges that viruses pose from sequence collection to extraction, to assembly and identification. Most tools - even now - focus primarily on virus identification, but there's more out there than just identifying viruses!
We develop tools and provide data and metadata resources specifically with virus ecology in mind. This project focuses on many of the challenges unique to virus biology, either by benchmarking general-purpose tools and identifying viral ecology friendly parameters, or develop tools specific to viruses and metagenomics that enhance data reuse and collaboration among virus researchers.
We integrate and leverage tools whose areas we lack expertise (e.g., assembly algorithms or read quality control) alongside our own tools, critically to maintain a processing pipeline's stability.
For developing new tools to address challenges we see in virus ecology, to integrate existing 3rd party tools (e.g., assembly tools or read QC), and to store datasets we feel is useful to the virus ecology field, we use cyberinfrastructure and platforms: CyVerse and KBase.
Both promote efficient data sharing, using common compute resources, and provide a resource for developers to securely build new Apps and data processing pipelines for virus ecology.
Even if we built and distributed these tools on a Bitbucket page with instructions (here), they'd help only the technically-minded labs, not the virus ecology community as a whole. By developing apps/tools and datasets on CyVerse and KBase, these free resources are made available to all viral ecology researchers. Even labs with minimal funding can entirely process an entire dataset - from raw reads to almost figures in a manuscript. It's not perfect, but we're moving in that direction.
We continue to add new apps across CyVerse and KBase, new datasets to CyVerse's Data Store, and are always looking for the latest and greatest virus ecology works.