miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines

Journal of computational biology: A journal of computational molecular cell biology

CarlosLijeron^1¹  ThahminaAli^1²  RajaMazumder^2³  ChangsuDong^1⁴  BaekdooKim^1⁵ 

[1] Address correspondence to: Dr. Konstantinos Krampis, Department of Biological Sciences, Hunter College of the City University of New York, 413 E 69th Street, Belfer Building, BRB-467F, New York, NY 10065-5024^4;Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, District of Columbia^2;Department of Biological Sciences, Hunter College of the City University of New York, New York, New York^5;Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York^3;Weill Cornell Medicine, Belfer Research Building, New York, New York^1

关键词: bioinformatics;    next-generation sequencing;    cloud computing;    Docker;    Galaxy;   

DOI  :  10.1089/cmb.2018.0218

学科分类：生物科学（综合）

来源: Mary Ann Liebert, Inc. Publishers

【 摘 要 】

The availability of low-cost small-factor sequencers, such as the Illumina MiSeq, MiniSeq, or iSeq, have paved the way for democratizing genomics sequencing, providing researchers in minority universities with access to the technology that was previously only affordable by institutions with large core facilities. However, these instruments are not bundled with software for performing bioinformatics data analysis, and the data analysis can be the main bottleneck for independent laboratories or even small clinical facilities that consider adopting genomic sequencing for medical applications. To address this issue, we have developedmiCloud, a bioinformatics platform that enables genomic data analysis through a fully featured data analysis cloud, which seamlessly integrates with genome sequencers over the local network. ThemiCloudcan be easily deployed without any prior bioinformatics expertise on any computing environment, from a laboratory computer workstation to a university computer cluster. Our platform not only provides access to a set of preconfigured RNA-Seq and CHIP-Seq bioinformatics pipelines, but also enables users to develop or install new preconfigured tools from the large selection available on open-source online Docker container repositories. ThemiCloudbuilt-in analysis pipelines are also integrated with the Visual Omics Explorer framework (Kim et al., 2016), which provides rich interactive visualizations and publication-ready graphics from the next-generation sequencing data. Ultimately, themiClouddemonstrates a bioinformatics approach that can be adopted in the field for standardizing genomic data analysis, similarly to the way molecular biology sample preparation kits have standardized laboratory operations.

【 授权许可】

Unknown