Repository: Freie Universit├Ąt Berlin, Math Department

A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping

Holtgrewe, M. and Emde, A.-K. and Weese, D. and Reinert, K. (2011) A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics, 12 (120). ISSN 1471-2105

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Official URL: http://dx.doi.org/10.1186/1471-2105-12-210

Abstract

Background Second generation sequencing technologies yield DNA sequence data at ultra high-throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. The assessment of the quality of read mapping results is not straightforward and has not been formalized so far. Hence, it has not been easy to compare different read mapping approaches in a unified way and to determine which program is the best for what task. Results We present a new benchmark method, called Rabema (Read Alignment BEnchMArk), for read mappers. It consists of a strict definition of the read mapping problem and of tools to evaluate the result of arbitrary read mappers supporting the SAM output format. Conclusions We show the usefulness of the benchmark program by performing a comparison of popular read mappers. The tools supporting the benchmark are licensed under the GPL and available from http://www.seqan.de/projects/rabema.html.

Item Type:Article
Subjects:Biological Sciences > Molecular Biology
Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:1072
Deposited By: Dipl. Inform. Manuel Holtgrewe
Deposited On:09 Jun 2011 13:52
Last Modified:27 Jun 2011 13:44

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