Searching for SNPs with cloud computing.
As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/.
Langmead
Ben
B
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA. blangmea@jhsph.edu
Schatz
Michael C
MC
Lin
Jimmy
J
Pop
Mihai
M
Salzberg
Steven L
SL
D000465:Algorithms; D000483:Alleles; D002875:Chromosomes / Q000648:ultrastructure; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D041321:Chromosomes, Human, X / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D003201:Computers; D006579:Heterozygote; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software