An integrated software for virus community sequencing data analysis

Mingjie Wang, Jianfeng Li, Xiaonan Zhang, Yue Han, Demin Yu, Donghua Zhang, Zhenghong Yuan, Zhitao Yang, Jinyan Huang, Xinxin Zhang

Research output: Contribution to journalReview articlepeer-review

1 Citation (Scopus)

Abstract

BACKGROUND: A virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases. However automatic and dedicated pipeline for interpreting virus community sequencing data has not been developed yet.

RESULTS: We developed Quasispecies Analysis Package (QAP), an integrated software platform to address the problems associated with making biological interpretations from massive viral population sequencing data. QAP provides quantitative insight into virus ecology by first introducing the definition "virus OTU" and supports a wide range of viral community analyses and results visualizations. Various forms of QAP were developed in consideration of broader users, including a command line, a graphical user interface and a web server. Utilities of QAP were thoroughly evaluated with high-throughput sequencing data from hepatitis B virus, hepatitis C virus, influenza virus and human immunodeficiency virus, and the results showed highly accurate viral quasispecies characteristics related to biological phenotypes.

CONCLUSIONS: QAP provides a complete solution for virus community high throughput sequencing data analysis, and it would facilitate the easy analysis of virus quasispecies in clinical applications.

Original languageEnglish
Pages (from-to)363
JournalBMC Genomics
Volume21
Issue number1
DOIs
Publication statusPublished - 15 May 2020
Externally publishedYes

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