Repository: Freie Universität Berlin, Math Department

RazerS - Fast Read Mapping with Sensitivity Control

Weese, D. and Emde, A.-K. and Rausch, T. and Döring, A. and Reinert, K. (2009) RazerS - Fast Read Mapping with Sensitivity Control. Genome Research, 19 (9). pp. 1646-1654.

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Second-generation sequencing technologies deliver DNA sequence data at unprecedented high throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. Due to the large amounts of data, efficient algorithms and implementations are crucial for this task. We present an efficient read mapping tool called RazerS. It allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. Our tool can work either lossless or with a user-defined loss rate at higher speeds. Given the loss rate, we present an approach that guarantees not to lose more reads than specified. This enables the user to adapt to the problem at hand and provides a seamless tradeoff between sensitivity and running time.

Item Type:Article
Subjects:Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:453
Deposited On:06 May 2009 09:46
Last Modified:03 Mar 2017 14:40

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