Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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).
22 references, click to expand
-
Space-efficient whole genome comparisons with Burrows-Wheeler transforms.J Comput Biol. 2005 May;12(4):407-15 PMID: 15882139
-
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.Nat Genet. 2008 Jun;40(6):722-9 PMID: 18438408
-
DNA sequencing. A plan to capture human diversity in 1000 genomes.Science. 2008 Jan 25;319(5862):395 PMID: 18218868
-
SOAP: short oligonucleotide alignment program.Bioinformatics. 2008 Mar 1;24(5):713-4 PMID: 18227114
-
Accurate whole human genome sequencing using reversible terminator chemistry.Nature. 2008 Nov 6;456(7218):53-9 PMID: 18987734
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores.Genome Res. 2008 Nov;18(11):1851-8 PMID: 18714091
-
Compressed indexing and local alignment of DNA.Bioinformatics. 2008 Mar 15;24(6):791-7 PMID: 18227115
-
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.Nature. 2008 Nov 6;456(7218):66-72 PMID: 18987736
-
SeqAn an efficient, generic C++ library for sequence analysis.BMC Bioinformatics. 2008 Jan 09;9:11 PMID: 18184432
-
Optimized design and assessment of whole genome tiling arrays.Bioinformatics. 2007 Jul 1;23(13):i195-204 PMID: 17646297
-
Using quality scores and longer reads improves accuracy of Solexa read mapping.BMC Bioinformatics. 2008 Feb 28;9:128 PMID: 18307793
-
PatternHunter: faster and more sensitive homology search.Bioinformatics. 2002 Mar;18(3):440-5 PMID: 11934743
-
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.Genome Res. 2008 Sep;18(9):1509-17 PMID: 18550803
-
The diploid genome sequence of an Asian individual.Nature. 2008 Nov 6;456(7218):60-5 PMID: 18987735
-
The transcriptional landscape of the yeast genome defined by RNA sequencing.Science. 2008 Jun 6;320(5881):1344-9 PMID: 18451266
-
Base-calling of automated sequencer traces using phred. II. Error probabilities.Genome Res. 1998 Mar;8(3):186-94 PMID: 9521922
-
Annotating large genomes with exact word matches.Genome Res. 2003 Oct;13(10):2306-15 PMID: 12975312
-
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.Nat Genet. 2008 Aug;40(8):987-93 PMID: 18660809
-
Identification of common molecular subsequences.J Mol Biol. 1981 Mar 25;147(1):195-7 PMID: 7265238
-
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.Nat Biotechnol. 2008 Jul;26(7):779-85 PMID: 18612301
-
ZOOM! Zillions of oligos mapped.Bioinformatics. 2008 Nov 1;24(21):2431-7 PMID: 18684737
-
Genome-wide mapping of in vivo protein-DNA interactions.Science. 2007 Jun 8;316(5830):1497-502 PMID: 17540862
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