eCite Digital Repository

Benchmarking undedicated cloud computing providers for analysis of genomic datasets

Citation

Yazar, S and Gooden, GEC and Mackey, DA and Hewitt, AW, Benchmarking undedicated cloud computing providers for analysis of genomic datasets, PLoS ONE, 9, (9) Article e108490. ISSN 1932-6203 (2014) [Refereed Article]


Preview
PDF
2Mb
  

Copyright Statement

Licensed under Creative Commons Attribution 3.0 Unported (CC BY 3.0) http://creativecommons.org/licenses/by/3.0/

DOI: doi:10.1371/journal.pone.0108490

Abstract

A major bottleneck in biological discovery is now emerging at the computational level. Cloud computing offers a dynamic means whereby small and medium-sized laboratories can rapidly adjust their computational capacity. We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets (E.coli CC102 strain and a Han Chinese male genome) and a standard bioinformatic pipeline on a Hadoop-based platform. Wall-clock time for complete assembly differed by 52.9% (95% CI: 27.5-78.2) for E.coli and 53.5% (95% CI: 34.4-72.6) for human genome, with GCE being more efficient than EMR. The cost of running this experiment on EMR and GCE differed significantly, with the costs on EMR being 257.3% (95% CI: 211.5-303.1) and 173.9% (95% CI: 134.6-213.1) more expensive for E.coli and human assemblies respectively. Thus, GCE was found to outperform EMR both in terms of cost and wall-clock time. Our findings confirm that cloud computing is an efficient and potentially cost-effective alternative for analysis of large genomic datasets. In addition to releasing our cost-effectiveness comparison, we present available ready-to-use scripts for establishing Hadoop instances with Ganglia monitoring on EC2 or GCE.

Item Details

Item Type:Refereed Article
Research Division:Medical and Health Sciences
Research Group:Ophthalmology and Optometry
Research Field:Ophthalmology
Objective Division:Health
Objective Group:Clinical Health (Organs, Diseases and Abnormal Conditions)
Objective Field:Hearing, Vision, Speech and Their Disorders
Author:Mackey, DA (Professor David Mackey)
Author:Hewitt, AW (Professor Alex Hewitt)
ID Code:97432
Year Published:2014
Web of Science® Times Cited:6
Deposited By:Menzies Institute for Medical Research
Deposited On:2014-12-17
Last Modified:2018-03-17
Downloads:210 View Download Statistics

Repository Staff Only: item control page