RazerS—fast read mapping with sensitivity control

• DOI: 10.1101/gr.088823.108
• Publication Date: 2009-07-11T00:45:21Z
• Authors: David Weese; Anne-Katrin Emde; Tobias Rausch; Andreas Döring; Knut Reinert
• Keywords: 0301 basic medicine; Time Factors; Genome, Human; Genome, Insect; Chromosome Mapping; Sequence Analysis, DNA; Sensitivity and Specificity; User-Computer Interface; 03 medical and health sciences; Drosophila melanogaster; Animals; Humans; Sequence Alignment; Algorithms; Software

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.