• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

快速病毒组探索者：一种用于宏基因组学数据中病毒和噬菌体鉴定及丰度分析的流程

FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.

作者信息

Tithi Saima Sultana, Aylward Frank O, Jensen Roderick V, Zhang Liqing

机构信息

Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.

Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America.

出版信息

PeerJ. 2018 Jan 12;6:e4227. doi: 10.7717/peerj.4227. eCollection 2018.

DOI:10.7717/peerj.4227
PMID:29340239
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5768174/
Abstract

With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.

摘要

随着下一代测序技术产生的宏基因组数据可用性的增加，迫切需要快速准确的工具来识别宿主相关和环境样本中的病毒。在本文中，我们开发了一个名为FastViromeExplorer的独立流程，通过对病毒和噬菌体序列数据库进行快速搜索，来检测和定量大型宏基因组数据集中病毒和噬菌体的丰度。来自人类微生物组和海洋环境样本的模拟数据和真实数据均用于验证FastViromeExplorer作为一种可靠工具，能够在大型数据集中快速准确地识别病毒及其丰度。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/2ac0286241ac/peerj-06-4227-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/3906d1b4d780/peerj-06-4227-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/391904e17691/peerj-06-4227-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/e442e54b06f0/peerj-06-4227-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/fc30768aa689/peerj-06-4227-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/2ac0286241ac/peerj-06-4227-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/3906d1b4d780/peerj-06-4227-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/391904e17691/peerj-06-4227-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/e442e54b06f0/peerj-06-4227-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/fc30768aa689/peerj-06-4227-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5691/5768174/2ac0286241ac/peerj-06-4227-g005.jpg

相似文献

1
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.快速病毒组探索者：一种用于宏基因组学数据中病毒和噬菌体鉴定及丰度分析的流程
PeerJ. 2018 Jan 12;6:e4227. doi: 10.7717/peerj.4227. eCollection 2018.
2
FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data.FastViromeExplorer-Novel：从宏基因组数据中恢复新型病毒和噬菌体的草图基因组。
J Comput Biol. 2023 Apr;30(4):391-408. doi: 10.1089/cmb.2022.0397. Epub 2023 Jan 6.
3
Computational approaches to predict bacteriophage-host relationships.预测噬菌体-宿主关系的计算方法。
FEMS Microbiol Rev. 2016 Mar;40(2):258-72. doi: 10.1093/femsre/fuv048. Epub 2015 Dec 9.
4
Virus detection in high-throughput sequencing data without a reference genome of the host.在没有宿主参考基因组的高通量测序数据中进行病毒检测。
Infect Genet Evol. 2018 Dec;66:180-187. doi: 10.1016/j.meegid.2018.09.026. Epub 2018 Oct 3.
5
Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types.用于从广泛宿主和样本类型中发现病毒的新型二代测序流程。
Virus Evol. 2020 Dec 2;6(2):veaa091. doi: 10.1093/ve/veaa091. eCollection 2020 Jul.
6
Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences.宏基因组学与核苷酸组成辅助新型噬菌体序列的鉴定及其宿主关联分析
Adv Biosyst. 2019 Nov;3(11):e1900108. doi: 10.1002/adbi.201900108. Epub 2019 Aug 16.
7
Application of next generation sequencing toward sensitive detection of enteric viruses isolated from celery samples as an example of produce.以芹菜样本中分离出的肠病毒为例，介绍下一代测序技术在敏感检测中的应用。
Int J Food Microbiol. 2017 Nov 16;261:73-81. doi: 10.1016/j.ijfoodmicro.2017.07.021. Epub 2017 Aug 3.
8
ViromeScan: a new tool for metagenomic viral community profiling.病毒组扫描：一种用于宏基因组病毒群落分析的新工具。
BMC Genomics. 2016 Mar 1;17:165. doi: 10.1186/s12864-016-2446-3.
9
ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads.ViraPipe：用于从下一代测序读取中进行病毒宏基因组分析的可扩展并行管道。
Bioinformatics. 2018 Mar 15;34(6):928-935. doi: 10.1093/bioinformatics/btx702.
10
PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets.噬菌体搜索器：在复杂基因组数据集中发现隐匿性病毒序列的管道。
Microb Genom. 2016 Mar 10;2(3):e000053. doi: 10.1099/mgen.0.000053. eCollection 2016 Mar.

引用本文的文献

1
Clinical metagenomics for diagnosis and surveillance of viral pathogens.用于病毒病原体诊断和监测的临床宏基因组学。
Nat Rev Microbiol. 2025 Aug 13. doi: 10.1038/s41579-025-01223-5.
2
Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.泥炭藓宏基因组中共享病毒序列的鉴定揭示了可能的泥炭藓核心病毒组的元素。
Environ Microbiome. 2025 Jun 5;20(1):62. doi: 10.1186/s40793-025-00719-0.
3
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.

本文引用的文献

1
Diel cycling and long-term persistence of viruses in the ocean's euphotic zone.昼夜节律循环和病毒在海洋真光层中的长期持久性。
Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11446-11451. doi: 10.1073/pnas.1714821114. Epub 2017 Oct 11.
2
Benchmarking viromics: an evaluation of metagenome-enabled estimates of viral community composition and diversity.病毒组学基准测试：对基于宏基因组学的病毒群落组成和多样性估计的评估
PeerJ. 2017 Sep 21;5:e3817. doi: 10.7717/peerj.3817. eCollection 2017.
3
Assembling metagenomes, one community at a time.
在单细胞分辨率下检测病毒序列可识别与宿主基因表达变化相关的新型病毒。
Nat Biotechnol. 2025 Apr 22. doi: 10.1038/s41587-025-02614-y.
4
Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.建立定量限的定量宏基因组学方法的开发及其在病毒中的应用。
Nucleic Acids Res. 2025 Feb 27;53(5). doi: 10.1093/nar/gkaf118.
5
Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.Virseqimprover：用于病毒重叠群纠错、延伸和注释的综合流程
PeerJ. 2025 Jan 10;13:e18515. doi: 10.7717/peerj.18515. eCollection 2025.
6
Blood virome research in myalgic encephalomyelitis/chronic fatigue syndrome: challenges and opportunities.肌痛性脑脊髓炎/慢性疲劳综合征的血液病毒组研究：挑战与机遇
Curr Opin Virol. 2024 Sep-Dec;68-69:101437. doi: 10.1016/j.coviro.2024.101437. Epub 2024 Nov 12.
7
Hecatomb: an integrated software platform for viral metagenomics.Hecatomb：病毒宏基因组学的集成软件平台。
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae020.
8
Identification and classification of the genomes of novel microviruses in poultry slaughterhouse.家禽屠宰场中新型微小病毒基因组的鉴定与分类
Front Microbiol. 2024 May 2;15:1393153. doi: 10.3389/fmicb.2024.1393153. eCollection 2024.
9
Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.探索谷物宏基因组学：解析微生物群落以增强粮食安全
Microorganisms. 2024 Mar 2;12(3):510. doi: 10.3390/microorganisms12030510.
10
Breeding honey bees ( L.) for low and high population growth: Gene expression of bees performing grooming behavior.培育用于低种群增长和高种群增长的蜜蜂（西方蜜蜂）：表现出清洁行为的蜜蜂的基因表达
Front Insect Sci. 2023 Mar 6;3:951447. doi: 10.3389/finsc.2023.951447. eCollection 2023.
一次组装一个群落的宏基因组。
BMC Genomics. 2017 Jul 10;18(1):521. doi: 10.1186/s12864-017-3918-9.
4
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.VirFinder：一种新型的基于 k-mer 的工具，用于从组装的宏基因组数据中识别病毒序列。
Microbiome. 2017 Jul 6;5(1):69. doi: 10.1186/s40168-017-0283-5.
5
Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.通过基因组解析宏基因组学追踪粪便微生物移植实验中的微生物定植。
Microbiome. 2017 May 4;5(1):50. doi: 10.1186/s40168-017-0270-x.
6
Ménage à trois in the human gut: interactions between host, bacteria and phages.人类肠道中的三人混战：宿主、细菌和噬菌体之间的相互作用。
Nat Rev Microbiol. 2017 Jul;15(7):397-408. doi: 10.1038/nrmicro.2017.30. Epub 2017 May 2.
7
Pseudoalignment for metagenomic read assignment.用于宏基因组读分配的伪比对。
Bioinformatics. 2017 Jul 15;33(14):2082-2088. doi: 10.1093/bioinformatics/btx106.
8
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.IMG/VR：一个包含培养和未培养的DNA病毒及逆转录病毒的数据库。
Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.
9
Viruses as Winners in the Game of Life.病毒：生命游戏中的赢家
Annu Rev Virol. 2016 Sep 29;3(1):197-214. doi: 10.1146/annurev-virology-100114-054952.
10
Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.全球丰富海洋病毒的生态基因组学及其潜在生物地球化学影响。
Nature. 2016 Sep 29;537(7622):689-693. doi: 10.1038/nature19366. Epub 2016 Sep 21.