Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

被引：16373

作者：

Langmead, Ben ^{[1
]}

Trapnell, Cole ^{[1
]}

Pop, Mihai ^{[1
]}

Salzberg, Steven L. ^{[1
]}

机构：

[1] Univ Maryland, Ctr Bioinformat & Computat Biol, Inst Adv Comp Studies, College Pk, MD 20742 USA

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 03期

基金：

美国国家科学基金会;

关键词：

IDENTIFICATION; SPACE;

D O I：

10.1186/gb-2009-10-3-r25

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

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