DOI: 10.1093/bioinformatics/btx153 ISSN:
GenomeScope: fast reference-free genome profiling from short reads
Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz- Computational Mathematics
- Computational Theory and Mathematics
- Computer Science Applications
- Molecular Biology
- Biochemistry
- Statistics and Probability
Abstract
Summary
GenomeScope 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.
Availability and Implementation
http://genomescope.org, https://github.com/schatzlab/genomescope.git.
Supplementary information
Supplementary data are available at Bioinformatics online.