A novel and well-defined benchmarking method for second generation read mapping

被引：53

作者：

Holtgrewe, Manuel ^{[1
]}

Emde, Anne-Katrin ^{[1
,2
]}

Weese, David ^{[1
]}

Reinert, Knut ^{[1
]}

机构：

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

[2] Max Planck Inst Mol Genet, D-14195 Berlin, Germany

来源：

BMC BIOINFORMATICS | 2011年 / 12卷

关键词：

GENOME; EFFICIENT; ALGORITHM; ULTRAFAST; ALIGNMENT; SEQUENCE;

D O I：

10.1186/1471-2105-12-210

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

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