Smolka, M., Rescheneder, P., Schatz, M. C., von Haeseler, A., Sedlazeck, F. J. (October 2015) Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol, 16 (1). p. 235. ISSN 1474-760X (Electronic)1474-7596 (Linking)
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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.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > Mapping and Rendering Investigative techniques and equipment > assays > next generation sequencing |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | Matt Covey |
| Date: | 22 October 2015 |
| Date Deposited: | 27 Oct 2015 19:26 |
| Last Modified: | 27 Oct 2015 19:26 |
| PMCID: | PMC4618857 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/31959 |
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