Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
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Open Access
- 4 March 2009
- journal article
- software
- Published by Springer Nature in Genome Biology
- Vol. 10 (3) , 1-10
- https://doi.org/10.1186/gb-2009-10-3-r25
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 http://bowtie.cbcb.umd.edu.Keywords
This publication has 24 references indexed in Scilit:
- Accurate whole human genome sequencing using reversible terminator chemistryNature, 2008
- The diploid genome sequence of an Asian individualNature, 2008
- DNA sequencing of a cytogenetically normal acute myeloid leukaemia genomeNature, 2008
- Mapping short DNA sequencing reads and calling variants using mapping quality scoresGenome Research, 2008
- ZOOM! Zillions of oligos mappedBioinformatics, 2008
- High-throughput sequencing provides insights into genome variation and evolution in Salmonella TyphiNature Genetics, 2008
- A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysisNature Biotechnology, 2008
- RNA-seq: An assessment of technical reproducibility and comparison with gene expression arraysGenome Research, 2008
- Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencingNature Genetics, 2008
- SOAP: short oligonucleotide alignment programBioinformatics, 2008