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

被引：161

作者：

Reid, Jeffrey G. ^{[1
]}

Carroll, Andrew ^{[2
]}

Veeraraghavan, Narayanan ^{[1
]}

Dahdouli, Mahmoud ^{[1
]}

Sundquist, Andreas ^{[2
]}

English, Adam ^{[1
]}

Bainbridge, Matthew ^{[1
]}

White, Simon ^{[1
]}

Salerno, William ^{[1
]}

Buhay, Christian ^{[1
]}

Yu, Fuli ^{[1
,3
]}

Muzny, Donna ^{[1
]}

Daly, Richard ^{[2
]}

Duyk, Geoff ^{[2
]}

Gibbs, Richard A. ^{[1
,3
]}

Boerwinkle, Eric ^{[1
,4
]}

机构：

[1] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA

[2] DNAnexus, Mountain View, CA 94040 USA

[3] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[4] Univ Texas Hlth Sci Ctr Houston, Ctr Human Genet, Houston, TX 77030 USA

来源：

BMC BIOINFORMATICS | 2014年 / 15卷

关键词：

NGS data; Variant calling; Annotation; Clinical sequencing; Cloud computing; READ ALIGNMENT; DISCOVERY; FRAMEWORK; GALAXY;

D O I：

10.1186/1471-2105-15-30

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

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.

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