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An integrated software for virus community sequencing data analysis
Mingjie Wang1, Jianfeng Li2, Xiaonan Zhang3
1Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.
We developed the Quasispecies Analysis Package (QAP), a software platform for analyzing virus community sequencing data. QAP offers quantitative insights into viral populations, aiding in understanding pathogenesis and treatment response.
Area of Science:
- Virology
- Bioinformatics
- Computational Biology
Background:
- Viral communities within hosts significantly impact disease progression and treatment outcomes.
- Existing methods lack automated pipelines for analyzing complex viral population sequencing data.
Purpose of the Study:
- To develop an integrated software platform for the comprehensive analysis of viral community sequencing data.
- To provide quantitative insights into viral ecology and quasispecies dynamics.
Main Methods:
- Development of the Quasispecies Analysis Package (QAP), a versatile software platform.
- Introduction of the "virus OTU" concept for quantitative viral community analysis.
- Implementation of command-line, GUI, and web server versions of QAP for broad accessibility.
Main Results:
- QAP enables quantitative analysis and visualization of viral community structures.
- Evaluation using hepatitis B, C, influenza, and HIV sequencing data demonstrated high accuracy.
- QAP accurately identified viral quasispecies characteristics linked to biological phenotypes.
Conclusions:
- QAP offers a complete solution for high-throughput sequencing data analysis in virology.
- The software facilitates straightforward analysis of viral quasispecies, with potential clinical applications.
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