Title :
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
fDate :
Nov. 30 2010-Dec. 3 2010
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;
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
DOI :
10.1109/CloudCom.2010.75
