Evidence map›Paper›PMID 32414327›Full record

ArticleBMC genomics2020

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

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 38% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 1 country.

Mingjie WangResearch Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.
Jianfeng LiState Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
Xiaonan ZhangKey Lab of Medicine Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, 200032, China.
Yue HanResearch Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.
Demin YuResearch Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.
Donghua ZhangResearch Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China.
Zhenghong YuanKey Lab of Medicine Molecular Virology of MOE/MOH, Shanghai Medical School, Fudan University, Shanghai, 200032, China.
Zhitao YangEmergency Department, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China. yangzhitao@hotmail.fr.
Jinyan HuangState Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China. jinyan@shsmu.edu.cn.
Xinxin ZhangResearch Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, 200025, China. zhangx@shsmu.edu.cn.ORCID http://orcid.org/0000-0002-0598-6425
Ruijin Hospital · CNShanghai Medical College of Fudan University · CN

Funding

Major National Projects for Infectious Diseases 2017ZX10202202National Key Research and Development Program 2016YFC0902800National Natural Science Foundation of China 81672069
6 · The paper itself

Abstract

backgroundA 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.

resultsWe 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.

conclusionsQAP 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.

Indexed as

SoftwareGenome, ViralGenomicsHumansQuasispeciesSequence AnalysisViromeVirus DiseasesVirusesHigh throughput sequencingPipelineVirus community

Identifiers

PMID32414327
PMCPMC7227348
OpenAlexW3026259741

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.