Biology subjects

Fritz J Sedlazeck

Publications and source records attributed to Fritz J Sedlazeck.

2 recordsLinked to original sources

bioRxiv2016

GenomeScope: Fast reference-free genome profiling from short reads

SummaryGenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate, and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels, and error rates.\n\nAvailability and Implementationhttp://genomescope.org, https://github.com/schatzlab/genomescope.git\n\nContactmschatz@jhu.edu.\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

Bioinformatics↗

bioRxiv2015

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 poorer quality assemblies, or for organisms with higher rates of mutations. 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 users dataset. Here we present Teaser, which 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. Using Teaser, we demonstrate how Bowtie2 can be optimized for different data.

Bioinformatics↗