RazerS-fast read mapping with sensitivity control

被引：97

作者：

Weese, David ^{[1
]}

Emde, Anne-Katrin ^{[1
]}

Rausch, Tobias ^{[2
]}

Doering, Andreas ^{[1
]}

Reinert, Knut ^{[1
]}

机构：

[1] Free Univ Berlin, Dept Comp Sci, D-14195 Berlin, Germany

[2] Int Max Planck Res Sch Computat Biol & Sci Comp, D-14195 Berlin, Germany

来源：

GENOME RESEARCH | 2009年 / 19卷 / 09期

关键词：

HUMAN GENOME; ALIGNMENT; EFFICIENT; DISCOVERY; SEQUENCE;

D O I：

10.1101/gr.088823.108

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：1646 / 1654

页数：9

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