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VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data
Darlene D Wagner1, Rachel L Marine2, Edward Ramos3
1Eagle Global Scientific LLC, Atlanta, Georgia, USA.
Microbiology Spectrum
|March 2, 2022
Summary
VPipe is an automated bioinformatics pipeline that simplifies viral genome assembly and data management from next-generation sequencing (NGS) data. This system enhances pathogen surveillance and public health responses to viral outbreaks.
Area of Science:
- Bioinformatics
- Virology
- Genomics
Background:
- Next-generation sequencing (NGS) generates vast amounts of data, posing challenges for viral pathogen analysis.
- Existing bioinformatics workflows can be complex and resource-intensive, creating bottlenecks for public health laboratories.
Purpose of the Study:
- To present VPipe, an automated bioinformatics pipeline for viral sequence analysis and data management.
- To streamline whole-genome assembly and species identification for viral pathogens using NGS data.
Main Methods:
- VPipe automates data quality control, genome assembly, and contig identification.
- A secure web-based portal provides an intuitive interface with advanced search functionalities.
- The system offers centralized data storage and analysis, overcoming infrastructure limitations.
Main Results:
- VPipe successfully generated high-quality viral genome assemblies for 12 public NGS datasets.
- The pipeline produced more contiguous assemblies compared to similar tools for respiratory syncytial virus and SARS-CoV-2.
- VPipe has been utilized by major public health institutions for characterizing thousands of clinical specimens.
Conclusions:
- VPipe effectively addresses computational and bioinformatics bottlenecks in viral pathogen analysis using NGS.
- The automated nature of VPipe accelerates public health responses to viral outbreaks and enhances pathogen surveillance capabilities.
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