Abstract
Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
Highlights
Improvements in the efficiency of DNA sequencing have both broadened the applications for sequencing and dramatically increased the size of sequencing datasets
Using Maq or SOAP for this purpose has been shown to be feasible by using multiple central processing unit (CPU), there is a clear need for new tools that consume less time and computational resources
SOAP could not be run on the PC because SOAP's memory footprint exceeds the PC's physical memory
Summary
Bowtie exhibits a large performance advantage over both Maq and SOAP when mapping reads to the human genome. Unlike SOAP, Bowtie's 1.3 GB memory footprint allows it to run on a typical PC with 2 GB of RAM. Performance results for running Bowtie v0.9.6 on the four-core server with one, two, and four threads. Performance results and memory footprints of running the Bowtie v0.9.6 indexer on the whole human genome (National Center for Biotechnology Information build 36.3, contigs). Bowtie's speed and small memory footprint are due to its use of the Burrows-Wheeler index in combination with the novel, quality-aware, backtracking algorithm introduced here. The following additional data are included with the online version of this article: a document containing supplementary discussions, tables, and figures pertaining to algorithms for navigating the Burrows-Wheeler transform, the full fourphase version of the alignment algorithm that incorporates the reverse-complement, index construction, and components of the index (Additional data file 1).
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