Fast and accurate long-read alignment with Burrows-Wheeler transform.
Fast and accurate long-read alignment with Burrows-Wheeler transform.
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DOI：
10.1093/bioinformatics/btp698
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发表时间：
2010-03-01
期刊：
影响因子：
--
通讯作者：
Durbin R
中科院分区：
文献类型：
--
作者：
Li H;Durbin R
动机：在过去的2年中，已经开发了许多用于将短测序读数与参考基因组进行比对的程序。它们中的大多数对于短读段是非常有效的，但是对于>200 bp的读段是低效的或不适用的，因为这些算法针对具有低测序错误率的短查询进行了大量和专门的调整。然而，一些测序平台已经产生了更长的读数，其他平台预计很快就会上市。对于较长的读取，基于散列的软件（如BLAT和SSAHA 2）仍然是唯一的选择。尽管如此，就每单位时间的比对碱基而言，这些方法比短读段比对器慢得多。结果如下：我们设计并实现了一种新的算法，Burrows-Wheeler Aligner的Smith-Waterman比对（BWA-SW），用于将长达1 Mb的长序列与具有几千兆字节内存的大型序列数据库（例如人类基因组）进行比对。该算法与SSAHA 2一样准确，比BLAT更准确，并且比两者都快几到几十倍。可用性：http://bio-bwa.sourceforge.net联系人：rd@sanger.ac.uk
Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk
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影响因子：
1.1
作者：
BLUMER, A;BLUMER, J;SEIFERAS, J
通讯作者：
SEIFERAS, J
影响因子：
3
作者：
Smith AD;Xuan Z;Zhang MQ
通讯作者：
Zhang MQ
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
1.7
作者：
Zhang, Z;Schwartz, S;Miller, W
通讯作者：
Miller, W
影响因子：
5.8
作者：
Jiang, Hui;Wong, Wing Hung
通讯作者：
Wong, Wing Hung