Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.
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.
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030, Vienna, Austria. moritz.smolka@univie.ac.at.
Moritz
M
Smolka
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030, Vienna, Austria. philipp.rescheneder@univie.ac.at.
Philipp
P
Rescheneder
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. mschatz@cshl.edu.|iPlant Collaborative/University of Arizona, Tuscon, AZ, 85719, USA. mschatz@cshl.edu.
Michael C
MC
Schatz
Center 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.|Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria. arndt.von.haeseler@univie.ac.at.
Arndt
A
von Haeseler
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. fsedlaze@cshl.edu.|iPlant Collaborative/University of Arizona, Tuscon, AZ, 85719, USA. fsedlaze@cshl.edu.
Fritz J
FJ
Sedlazeck
D000818:Animals; D019985:Benchmarking; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010473:Perciformes / Q000235:genetics; D016415:Sequence Alignment; D012984:Software