GASSST: global alignment short sequence search tool.
GASSST: global alignment short sequence search tool.
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DOI：
10.1093/bioinformatics/btq485
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发表时间：
2010-10-15
期刊：
影响因子：
--
通讯作者：
Lavenier D
中科院分区：
文献类型：
--
作者：
Rizk G;Lavenier D
动机：能够产生大量序列数据的下一代测序技术的快速发展正在导致广泛的新应用。这引发了对快速准确的对准软件的需求。常见的技术通常限制比对中的插入缺失以提高速度，而更灵活的比对器对于大规模应用来说太慢了。此外，随着生成的读段越来越大，许多当前的比对器变得低效。因此，我们的新比对器GASSST（全局比对短序列搜索工具）的目标是实现2倍的高性能，对indel的数量没有限制，设计对长读段仍然有效。结果如下：我们提出了一个新的有效的过滤步骤，丢弃大多数对齐来自种子阶段之前，他们是昂贵的动态规划算法检查。我们使用一系列精心设计的过滤器，增加了复杂性和效率，以快速消除大多数候选人的路线在广泛的配置。主过滤器使用一个预先计算的表，其中包含相互对齐的短四个基本单词的对齐分数。该表被设计为近似全动态规划算法的分数的新算法重复使用多次。我们比较了GASSST与BWA，BFAST，SSAHA 2和PASS的性能。我们发现，GASSST实现了高灵敏度，在广泛的配置和更快的整体执行时间比其他国家的最先进的对准。可用性：GASSST是根据CeCILL软件许可证在http://www.irisa.fr/symbiose/projects/gassst/上分发的。联系人：guillaume. irisa.fr; dominique. irisa.fr补充信息：补充数据可在生物信息学在线上获得。
Motivation: The rapid development of next-generation sequencing technologies able to produce huge amounts of sequence data is leading to a wide range of new applications. This triggers the need for fast and accurate alignment software. Common techniques often restrict indels in the alignment to improve speed, whereas more flexible aligners are too slow for large-scale applications. Moreover, many current aligners are becoming inefficient as generated reads grow ever larger. Our goal with our new aligner GASSST (Global Alignment Short Sequence Search Tool) is thus 2-fold—achieving high performance with no restrictions on the number of indels with a design that is still effective on long reads. Results: We propose a new efficient filtering step that discards most alignments coming from the seed phase before they are checked by the costly dynamic programming algorithm. We use a carefully designed series of filters of increasing complexity and efficiency to quickly eliminate most candidate alignments in a wide range of configurations. The main filter uses a precomputed table containing the alignment score of short four base words aligned against each other. This table is reused several times by a new algorithm designed to approximate the score of the full dynamic programming algorithm. We compare the performance of GASSST against BWA, BFAST, SSAHA2 and PASS. We found that GASSST achieves high sensitivity in a wide range of configurations and faster overall execution time than other state-of-the-art aligners. Availability: GASSST is distributed under the CeCILL software license at http://www.irisa.fr/symbiose/projects/gassst/ Contact: guillaume.rizk@irisa.fr; dominique.lavenier@irisa.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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