Howdah - A Flexible Pipeline Framework for Analyzing Genomic Data

Author

Lewis, Steven ; Reynolds, Sheila ; Rovera, Hector ; O´Leary, Mike ; Killcoyne, Sarah ; Shmulevich, Ilya ; Boyle, John

Author_Institution

Inst. for Syst. Biol., Seattle, WA, USA

fYear

2010

fDate

Nov. 30 2010-Dec. 3 2010

Firstpage

776

Lastpage

779

Abstract

The advent of new high-throughput sequencing technologies has led to a flood of genomic data which overwhelms the capabilities of single processor machines. We present a MapReduce pipeline called Howdah that supports the analysis of genomic sequence data allowing multiple tests to be plugged in to a single MapReduce job. The pipeline is used to detect chromosomal abnormalities such as insertions, deletions and translocations as well as single nucleotide polymorphisms (SNPs).

Keywords

bioinformatics; cloud computing; data analysis; genomics; parallel processing; Howdah; MapReduce pipeline; bioinformatics; chromosomal abnormalities; cloud computing; flexible pipeline framework; genomic sequence data analysis; high-throughput sequencing technologies; parallel processing; single nucleotide polymorphisms; single processor machines; Bioinformatics; Cancer; Data mining; Genomics; Pipelines; Registers; Testing; Hadoop; MapReduce; bioinformatics; cloud computing; genomics; parallelization;

fLanguage

English

Publisher

ieee

Conference_Titel

Cloud Computing Technology and Science (CloudCom), 2010 IEEE Second International Conference on

Conference_Location

Indianapolis, IN

Print_ISBN

978-1-4244-9405-7

Electronic_ISBN

978-0-7695-4302-4

Type

conf

DOI

10.1109/CloudCom.2010.75

Filename

5708530