Fast and accurate short read alignment with Burrows-Wheeler transform.
Fast and accurate short read alignment with Burrows-Wheeler transform.
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DOI：
10.1093/bioinformatics/btp324
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发表时间：
2009-07-15
期刊：
影响因子：
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通讯作者：
Durbin R
中科院分区：
文献类型：
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作者：
Li H;Durbin R
动机：新的DNA测序技术产生了大量的短读，要求开发快速准确的读比对程序。第一代基于哈希表的方法已经开发出来，包括MAQ，它准确、功能丰富、速度足够快，可以对来自单个个体的短读取进行对齐。然而，MAQ不支持单端读取的间隙对齐，这使得它不适合经常出现索引的较长读取的对齐。当校准规模扩大到数百个个体的重测序时，MAQ的速度也是一个问题。结果：我们实现了Burrows-Wheeler比对工具（BWA），这是一种基于Burrows-Wheeler Transform （BWT）的反向搜索的新型reads比对包，可以有效地将短测序reads与大型参考序列（如人类基因组）进行比对，从而允许错配和空白。BWA支持碱基空间读取，例如来自Illumina测序机，以及来自AB SOLiD机器的彩色空间读取。对模拟和真实数据的评估表明，BWA比MAQ快10 - 20倍，同时达到相似的精度。此外，BWA以新的标准SAM（序列对齐/映射）格式输出对齐。在对齐之后，变体调用和其他下游分析可以使用开源SAMtools软件包来实现。可用性：http://maq.sourceforge.net联系方式：rd@sanger.ac.uk
Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk