Rabema

Abstract

Rabema is a program that supports a new read mapper benchmark methodology. The methodology is based on a strict definition of the read mapping problem and allows the evaluation of arbitrary read mapping programs that create SAM output. The paper gives an explanation of the theory behind the benchmark methodology with an example evaluation.

Additional Online Material

• Rabema Online Manual
• Rabema Command Line Interface
• Description of Rabema Reports

Links

• Download binaries
• View the source code and README on GitHub

Please Cite

• M. Holtgrewe, A.-K. Emde, D. Weese, K. Reinert, “A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping”, vol. 12, iss. 120, 2011-05-26.
  cite this publication

  @article{fu_mi_publications1072,
   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.},
   author = {M. Holtgrewe and A.-K. Emde and D. Weese and K. Reinert},
   journal = {BMC Bioinformatics},
   month = {May},
   number = {120},
   publisher = {BioMed Central},
   title = {A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping},
   url = {http://publications.imp.fu-berlin.de/1072/},
   volume = {12},
   year = {2011}
  }

Contact

For questions, comments, or suggestions please contact:

Manuel Holtgrewe