Ultrafast and memory-efficient alignment of short DNA sequences to the human genome 英文参考文献.docVIP

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome 英文参考文献.doc

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome 英文参考文献

Open Access So 2009LangmeadetVoal.lumeftw10,areIssue 3, Article R25 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Ben Langmead, Cole Trapnell, Mihai Pop and Steven L Salzberg Address: Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA. Correspondence: Ben Langmead. Email: langmead@ Published: 4 March 2009 Received: 21 October 2008 Revised: 19 December 2008 Accepted: 4 March 2009 Genome Biology 2009, 10:R25 (doi:10.1186/gb-2009-10-3-r25) The electronic version of this article is the complete one and can be found online at /2009/10/3/R25 ? 2009 Langmead et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Bowtie:pBowshort-readtie: a new ualignmentltrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes./p Abstract Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source . Rationale sequence a total of about six trillion base pairs of human DNA [9]. Improvements in the efficiency of DNA sequencing have both broadened the applications for sequencing and dramatically increased the size of sequencing datasets. Technologies from Illumina (San Diego, CA, USA) and Applied Biosystems (Fos