Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

BMC Bioinformatics

Jeffrey G Reid⁴  Andrew Carroll¹  Narayanan Veeraraghavan⁴  Mahmoud Dahdouli⁴  Andreas Sundquist¹  Adam English⁴  Matthew Bainbridge⁴  Simon White⁴  William Salerno⁴  Christian Buhay⁴  Fuli Yu³  Donna Muzny⁴  Richard Daly¹  Geoff Duyk¹  Richard A Gibbs³  Eric Boerwinkle² 

[1] DNAnexus, Mountain View, CA 94040, USA

[2] Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA

[3] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

[4] Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

关键词: Cloud computing;    Clinical sequencing;    Annotation;    Variant calling;    NGS data;   

Others  :  1087637
DOI  :  10.1186/1471-2105-15-30

 received in 2013-09-17, accepted in 2014-01-20,  发布年份 2014

【 摘 要 】

Background

Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results.

Results

To address these challenges, we have developed the Mercury analysis pipeline and deployed it in local hardware and the Amazon Web Services cloud via the DNAnexus platform. Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts.

Conclusions

By taking advantage of cloud computing and with Mercury implemented on the DNAnexus platform, we have demonstrated a powerful combination of a robust and fully validated software pipeline and a scalable computational resource that, to date, we have applied to more than 10,000 whole genome and whole exome samples.

【 授权许可】

   
2014 Reid et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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