CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

BMC Genomics

Software

Ricky S. Adkins¹  Sonia Agrawal¹  Anup Mahurkar¹  Samuel V. Angiuoli¹  Cesar Arze¹  Jonathan Crabtree¹  Mahesh Vangala¹  Kevin Galens¹  David Riley¹  Owen White²  Claire M. Fraser³  Hervé Tettelin³  W. Florian Fricke⁴ 

[1] Institute for Genome Sciences, Baltimore, MD, USA;Institute for Genome Sciences, Baltimore, MD, USA;Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA;Institute for Genome Sciences, Baltimore, MD, USA;Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA;Institute for Genome Sciences, Baltimore, MD, USA;Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA;Department of Nutrigenomics, University of Hohenheim, Stuttgart, Germany;

关键词: Comparative genomics;    Microbial genomics;    Automated analysis;    Whole-genome alignment;    Bioinformatics resource;    Virtual machine;    Cloud computing;   

DOI  :  10.1186/s12864-017-3717-3

 received in 2017-03-27, accepted in 2017-04-21,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsCloVR-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.ConclusionsCloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.

【 授权许可】

CC BY   
© The Author(s). 2017