Open Access Highly Accessed Methodology article

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

Manuel Holtgrewe1*, Anne-Katrin Emde12, David Weese1 and Knut Reinert1

Author affiliations

1 Department of Computer Science, Free University of Berlin, Takustr. 9, 14195 Berlin, Germany

2 Max-Planck-Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany

For all author emails, please log on.

Citation and License

BMC Bioinformatics 2011, 12:210  doi:10.1186/1471-2105-12-210

Published: 26 May 2011



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.


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.


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 webcite.