VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
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DOI：
10.1186/s12859-019-2606-y
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发表时间：
2019-01-23
影响因子：
3
通讯作者：
Greninger, Alexander L.
中科院分区：
文献类型：
--
作者：
Shean, Ryan C.;Makhsous, Negar;Greninger, Alexander L.
随着测序技术变得越来越便宜和容易使用，更多的团体能够获得具有公共卫生和科学重要性的病毒的全基因组序列。向NCBI GenBank提交基因组数据是出版前的一项要求，在公开科学数据方面发挥着关键作用。GenBank目前有自动原核和真核基因组注释管道，但没有流感病毒以外的病毒注释管道。注释和提交的病毒基因组序列是一个不平凡的任务，特别是对于那些不经常与GenBank互动的数据submissions.ResultsWe提出病毒注释管道和iDentification（VAPiD），一个便携式和轻量级的命令行工具注释和GenBank沉积的病毒基因组。VAPiD支持几乎所有未分段病毒基因组的注释。已对人免疫缺陷病毒、人副流感病毒1-4、人偏肺病毒、人冠状病毒（229 E/OC 43/NL 63/HKU 1/SARS/MERS）、人肠道病毒/鼻病毒、麻疹病毒、腮腺炎病毒、甲型-戊型肝炎病毒、基孔肯雅病毒、登革热病毒和西尼罗河病毒以及人多瘤病毒BK/JC/MCV、人腺病毒和人乳头瘤病毒进行了验证。该程序可以处理不同病毒向GenBank的单个或批量提交，并正确注释多个病毒，包括那些包含核糖体滑移或RNA编辑的病毒，而无需事先了解要注释的病毒。VAPiD是用Python编程，并与Windows，Linux，和Mac OS systems.ConclusionsWe兼容，创建了一个便携式的，轻量级的，用户友好的，支持互联网的，开源的，命令行基因组注释和提交包，以促进病毒基因组提交到NCBI GenBank。有关下载和安装VAPiD的说明，请访问https://github.com/rcs333/VAPiD。
BackgroundWith sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.ResultsWe present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1-4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems.ConclusionsWe have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found at https://github.com/rcs333/VAPiD.
影响因子：
5.3
作者：
Greninger AL;Pepper G;Shean RC;Cent A;Palileo I;Kuypers JM;Schiffer JT;Jerome KR
通讯作者：
Jerome KR