Efficient alignment of next generation sequencing data using MapReduce on the cloud

Rawan T. Al Saad, Qutaibah Malluhi, Mohamed Abouelhoda

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

This paper presents a methodology for running NGS read mapping tools in the cloud environment based on the MapReduce programming paradigm. As a demonstration, the recently developed and robust sequence alignment tool, BFAST, is used within our methodology to handle massive datasets. The results of our experiments show that the transformation of existing read mapping tools to run within the MapReduce framework dramatically reduces the total execution time and enables the user to utilize the resources provided by the cloud.

Original languageEnglish
Title of host publication2012 Cairo International Biomedical Engineering Conference, CIBEC 2012
Pages18-22
Number of pages5
DOIs
Publication statusPublished - 1 Dec 2012
Externally publishedYes
Event2012 Cairo International Biomedical Engineering Conference, CIBEC 2012 - Giza, Egypt
Duration: 20 Dec 201222 Dec 2012

Other

Other2012 Cairo International Biomedical Engineering Conference, CIBEC 2012
CountryEgypt
CityGiza
Period20/12/1222/12/12

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Demonstrations
Experiments

Keywords

  • bioinformatics
  • Cloud computing
  • MapReduce
  • sequence alignment

ASJC Scopus subject areas

  • Biomedical Engineering

Cite this

Al Saad, R. T., Malluhi, Q., & Abouelhoda, M. (2012). Efficient alignment of next generation sequencing data using MapReduce on the cloud. In 2012 Cairo International Biomedical Engineering Conference, CIBEC 2012 (pp. 18-22). [6473312] https://doi.org/10.1109/CIBEC.2012.6473312

Efficient alignment of next generation sequencing data using MapReduce on the cloud. / Al Saad, Rawan T.; Malluhi, Qutaibah; Abouelhoda, Mohamed.

2012 Cairo International Biomedical Engineering Conference, CIBEC 2012. 2012. p. 18-22 6473312.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Al Saad, RT, Malluhi, Q & Abouelhoda, M 2012, Efficient alignment of next generation sequencing data using MapReduce on the cloud. in 2012 Cairo International Biomedical Engineering Conference, CIBEC 2012., 6473312, pp. 18-22, 2012 Cairo International Biomedical Engineering Conference, CIBEC 2012, Giza, Egypt, 20/12/12. https://doi.org/10.1109/CIBEC.2012.6473312
Al Saad RT, Malluhi Q, Abouelhoda M. Efficient alignment of next generation sequencing data using MapReduce on the cloud. In 2012 Cairo International Biomedical Engineering Conference, CIBEC 2012. 2012. p. 18-22. 6473312 https://doi.org/10.1109/CIBEC.2012.6473312
Al Saad, Rawan T. ; Malluhi, Qutaibah ; Abouelhoda, Mohamed. / Efficient alignment of next generation sequencing data using MapReduce on the cloud. 2012 Cairo International Biomedical Engineering Conference, CIBEC 2012. 2012. pp. 18-22
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