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Genome Biol. 2015 Oct 22;16:235. doi: 10.1186/s13059-015-0803-1.

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.

Author information

  • 1Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030, Vienna, Austria. moritz.smolka@univie.ac.at.
  • 2Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030, Vienna, Austria. philipp.rescheneder@univie.ac.at.
  • 3Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. mschatz@cshl.edu.
  • 4iPlant Collaborative/University of Arizona, Tuscon, AZ, 85719, USA. mschatz@cshl.edu.
  • 5Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030, Vienna, Austria. arndt.von.haeseler@univie.ac.at.
  • 6Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria. arndt.von.haeseler@univie.ac.at.
  • 7Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. fsedlaze@cshl.edu.
  • 8iPlant Collaborative/University of Arizona, Tuscon, AZ, 85719, USA. fsedlaze@cshl.edu.

Abstract

Mapping reads to a genome remains challenging, especially for non-model organisms with lower quality assemblies, or for organisms with higher mutation rates. While most research has focused on speeding up the mapping process, little attention has been paid to optimize the choice of mapper and parameters for a user's dataset. Here, we present Teaser, a software that assists in these choices through rapid automated benchmarking of different mappers and parameter settings for individualized data. Within minutes, Teaser completes a quantitative evaluation of an ensemble of mapping algorithms and parameters. We use Teaser to demonstrate how Bowtie2 can be optimized for different data.

PMID:
26494581
PMCID:
PMC4618857
DOI:
10.1186/s13059-015-0803-1
[PubMed - indexed for MEDLINE]
Free PMC Article
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