CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.
CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.
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DOI：
10.1186/s12864-017-3717-3
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发表时间：
2017-04-27
期刊：
影响因子：
4.4
通讯作者：
Fricke WF
中科院分区：
文献类型：
--
作者：
Agrawal S;Arze C;Adkins RS;Crabtree J;Riley D;Vangala M;Galens K;Fraser CM;Tettelin H;White O;Angiuoli SV;Mahurkar A;Fricke WF
增加基因组序列数据对科学界的好处取决于易于使用，可扩展的生物信息学支持。CloVR-Comparative将常用的生物信息学工具结合到一个直观、自动化和云支持的分析管道中，用于比较微生物基因组学。CloVR-Comparative运行在注释的完整或草图基因组序列上，这些序列由用户上传或通过基于分类树的用户界面选择并从NCBI下载。CloVR-Comparative运行无参考的多个全基因组比对，以确定独特的，共享的和核心的编码序列（CDS）和单核苷酸多态性（SNP）。输出包括简短的摘要报告和详细的基于文本的结果文件，图形可视化（系统发育树，圆形图），以及链接到Sybil比较基因组浏览器的数据库文件。数据上传和下载、管道配置和监控以及对Sybil的访问都通过CloVR-Comparative Web界面进行管理。CloVR-Comparative和Sybil作为CloVR虚拟设备的一部分分发，该虚拟设备在本地计算机或Amazon EC2云上运行。代表性数据集（例如40个草稿和完整的大肠杆菌基因组）在本地桌面上处理不到36小时，在EC2上处理成本不到20美元。CloVR-Comparative允许任何可以访问互联网的人运行比较基因组学项目，同时消除了对现场计算资源和专业知识的需求。本文的在线版本（doi：10.1186/s12864-017-3717-3）包含补充材料，可供授权用户使用。
The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise. The online version of this article (doi:10.1186/s12864-017-3717-3) contains supplementary material, which is available to authorized users.