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

doi:10.1186/s12864-020-6744-4

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 journal › Review article › peer-review

3 Citations (Scopus)

70 Downloads (Pure)

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 language	English
Article number	363
Pages (from-to)	1-10
Number of pages	10
Journal	BMC Genomics
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s12864-020-6744-4
Publication status	Published - 15 May 2020
Externally published	Yes

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1186/s12864-020-6744-4Licence: CC BY

ArticleFinal published version, 3.18 MBLicence: CC BY

Cite this

@article{4b832ff46c4b43558723b90fe77b412a,

title = "An integrated software for virus community sequencing data analysis",

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.",

keywords = "Genome, Viral/genetics, Genomics/methods, Humans, Quasispecies, Sequence Analysis, Software, Virome/genetics, Virus Diseases/virology, Viruses/classification, Virus community, High throughput sequencing, Pipeline",

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

year = "2020",

month = may,

day = "15",

doi = "10.1186/s12864-020-6744-4",

language = "English",

volume = "21",

pages = "1--10",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central",

number = "1",

}

TY - JOUR

T1 - An integrated software for virus community sequencing data analysis

AU - Wang, Mingjie

AU - Li, Jianfeng

AU - Zhang, Xiaonan

AU - Han, Yue

AU - Yu, Demin

AU - Zhang, Donghua

AU - Yuan, Zhenghong

AU - Yang, Zhitao

AU - Huang, Jinyan

AU - Zhang, Xinxin

PY - 2020/5/15

Y1 - 2020/5/15

N2 - 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.

AB - 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.

KW - Genome, Viral/genetics

KW - Genomics/methods

KW - Humans

KW - Quasispecies

KW - Sequence Analysis

KW - Software

KW - Virome/genetics

KW - Virus Diseases/virology

KW - Viruses/classification

KW - Virus community

KW - High throughput sequencing

KW - Pipeline

UR - http://www.scopus.com/inward/record.url?scp=85084785882&partnerID=8YFLogxK

U2 - 10.1186/s12864-020-6744-4

DO - 10.1186/s12864-020-6744-4

M3 - Review article

C2 - 32414327

SN - 1471-2164

VL - 21

SP - 1

EP - 10

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 363

ER -

An integrated software for virus community sequencing data analysis

Abstract

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this