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Protocols

Follow user guides and process viral data
with these best-practice guides

iVirus Protocols

These protocols and workflows below provide step-by-step examples for using iVirus-enabled apps across CyVerse and KBase. These protocols use apps that were integrated by the iVirus team or other developers at CyVerse or KBase.

Protocols Using CyVerse

CyVerse lacks a mechanism for aggregating data, apps, and "meta-information" (though you can share analyses), so iVirus uses protocols.io to provide an easy-to-use means to organize all the resources users need to run an analysis.

Processing a Viral Metagenome

In protocols.io, a collection refers to a group of protocols. They can be related protocols (e.g. viral extraction methods) or a series of protocols to be completed in order (e.g., a processing pipeline). Here, we have a single collection that the user can use to process a viral metagenome from raw metagenomic reads all the way to viral sequences with preliminary taxonomic classification and clustering.

Download raw reads from SRA, clean the reads, assemble, identify viruses, check the quality of the viruses, and identify their taxonomy!

Individual protocols

If you already know which protocol you want to use, see below!

Download viral genomic reads from the SRA

Use Trimmomatic to remove adapters and low-quality bases

Run MetaSPAdes against the cleaned reads to assemble them into contigs

Use VirSorter1 to identify viral sequences within assembled contigs. Select from 3 confidence categories and prophage versus non-prophage viruses

If using an older version of vConTACT2, prepare data for it using a FASTA-formatted amino acid file

Run vConTACT2 on a viral dataset and visualize the results in Cytoscape

Mapping Metagenomic Reads

Take a set of reads and align them against a set of viral genomes to generate relative abundances

Protocols Using KBase

KBase uses "Narratives", which serve as lab notebooks to organize data, analyses, and any other information the author wishes to add regarding the experiment. This allows for reproducible workflows, and effectively mirrors much of the functionality of protocols.io.

Processing a Viral Metagenome in KBase

Check here to be taken to the KBase narrative to process a viral metagenome, or browse below to look over the entire narrative.

A few things to note:

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