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

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)

[thumbnail of Paper]
PDF (Paper)
Schatz Genome Biology 2015c.pdf - Published Version

Download (766kB) | Preview
URL: http://www.ncbi.nlm.nih.gov/pubmed/26494581
DOI: 10.1186/s13059-015-0803-1


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

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving