RazerS—fast read mapping with sensitivity control
- 1 Department of Computer Science, Free University of Berlin, 14195 Berlin, Germany;
- 2 International Max Planck Research School for Computational Biology and Scientific Computing, 14195 Berlin, Germany
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.
Footnotes
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↵3 Corresponding author.
E-mail weese{at}inf.fu-berlin.de; fax 49-30-83875218.
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[RazerS is freely available at http://www.seqan.de/projects/razers.html.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.088823.108.
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- Received November 2, 2008.
- Accepted April 29, 2009.
- Copyright © 2009 by Cold Spring Harbor Laboratory Press
