Fast and accurate read mapping with approximate seeds and multiple backtracking.
Fast and accurate read mapping with approximate seeds and multiple backtracking.
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DOI：
10.1093/nar/gkt005
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发表时间：
2013-04
影响因子：
14.9
通讯作者：
Reinert K
中科院分区：
文献类型：
--
作者：
Siragusa E;Weese D;Reinert K
我们提出了马赛，读映射器代表国家的最先进的速度和准确性。我们的工具比RazerS 3和mrFAST快一个数量级，比Bowtie 2和BWA快2-4倍，更准确。我们的读映射器的新颖之处是过滤近似种子和多个回溯的方法。与精确种子相比，近似种子在保持灵敏度的同时提高了过滤特异性。多重回溯通过利用下一代测序数据的重复性来分摊搜索大量种子的成本。结合在一起，这两种方法显着加快基因组数据集上的近似搜索。Masai是使用SeqAn库在C++中实现的。源代码是在BSD许可证下发布的，Linux、Mac OS X和Windows的二进制文件可以从http://www.seqan.de/projects/masai免费下载。
We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2–4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai.
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