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arXiv · 1208.4238

Fast and sensitive read mapping with approximate seeds and multiple backtracking

Enrico Siragusa·David Weese·Knut Reinert
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Abstract

We present Masai, a read mapper representing the state of the art in terms of speed and sensitivity. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2--3 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 to 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 datasets. 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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Enrico Siragusa, David Weese, Knut Reinert. 2012-08-21. Fast and sensitive read mapping with approximate seeds and multiple backtracking. https://arxiv.org/abs/1208.4238

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