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Cold Spring Harbor Laboratory Press, Genome Research, 9(19), p. 1646-1654, 2009

DOI: 10.1101/gr.088823.108

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RazerS—fast read mapping with sensitivity control

Journal article published in 2009 by David Weese, Anne-Katrin Emde, Tobias Rausch ORCID, Andreas Döring, Knut Reinert
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Data provided by SHERPA/RoMEO

Abstract

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.