Supporting materials for: "VirAmp: A Galaxy-based viral genome assembly pipeline".

Dataset type: Software, Workflow, Virtual-Machine
Data released on April 21, 2015

Wan Y; Renner DW; Albert I; Szpara ML (2015): Supporting materials for: "VirAmp: A Galaxy-based viral genome assembly pipeline". GigaScience Database. http://dx.doi.org/10.5524/100113

DOI10.5524/100113

We have developed a multi-step viral genome assembly pipeline named VirAmp, that combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices into a single, easy to use interface. We tested our pipeline with three different datasets from human herpes simplex virus (HSV).
VirAmp provides a user-friendly interface and a complete pipeline for viral genome analysis. We make our software available via an Amazon Elastic Cloud disk image that can be easily launched by anyone with an Amazon web service account. A demonstration version of our system can be found at http://viramp.com. We also maintain detailed documentation on each tool and methodology at http://docs.viramp.com.
Here in GigaDB you will find an archived version of the tools as they were published.

Additional details

Read the peer-reviewed publication(s):

Wan, Y., Renner, D. W., Albert, I., & Szpara, M. L. (2015). VirAmp: a galaxy-based viral genome assembly pipeline. GigaScience, 4(1). doi:10.1186/s13742-015-0060-y

Additional information:

http://viramp.com





File NameSample IDData TypeFile FormatSizeRelease Date 
Genome sequenceFASTQ61.28 MB2015-04-21
Genome sequenceFASTQ61.28 MB2015-04-21
OtherUNKNOWN2.56 GB2015-04-21
OtherUNKNOWN7.3 GB2015-04-21
Galaxy workflowGalaxy workflow13.84 KB2015-04-21
Genome sequenceFASTQ3.54 GB2014-11-05
Genome sequenceFASTQ3.48 GB2014-11-05
Genome sequenceFASTQ1.49 GB2014-11-05
Genome sequenceFASTQ1.47 GB2014-11-05
Genome sequenceFASTQ1.28 GB2014-11-05
Displaying 1-10 of 15 File(s).
Date Action
April 27, 2015 Dataset publish