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VirAmp: a galaxy-based viral genome assembly pipeline
Yinan Wan1, Daniel W Renner2, Istvan Albert3
1The Huck Institutes of the Life Sciences, University Park, PA 16802 USA.
Gigascience
|April 29, 2015
Summary
VirAmp is a new web-based pipeline that simplifies viral genome assembly and analysis. This tool makes complex bioinformatics accessible to more labs, enabling efficient interpretation of next-generation sequencing data.
Area of Science:
- Bioinformatics
- Genomics
- Virology
Background:
- Next-generation sequencing (NGS) enables rapid, high-coverage sequencing of numerous viral strains.
- Limited accessibility of command-line bioinformatics tools hinders viral genome assembly and variation analysis in individual labs.
Purpose of the Study:
- To develop an accessible, user-friendly bioinformatics pipeline for viral genome analysis.
- To integrate existing tools and best practices into a streamlined workflow.
Main Methods:
- Development of VirAmp, a multi-step viral genome assembly pipeline.
- Implementation of a web-enabled Galaxy interface for user accessibility.
- Testing the pipeline using human herpes simplex virus (HSV) datasets.
Main Results:
- VirAmp successfully assembles, analyzes, and interprets high-coverage viral sequencing data.
- The pipeline offers ease and efficiency previously unavailable for viral genome analysis.
- Automates best-practice bioinformatics workflows into a single, intuitive interface.
Conclusions:
- VirAmp provides a user-friendly, comprehensive solution for viral genome analysis.
- The software is available as a cloud disk image for easy deployment.
- A demonstration instance and detailed documentation are provided for user support.
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