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

doi:10.1093/bioinformatics/btx153

GenomeScope: fast reference-free genome profiling from short reads

Bioinformatics. 2017 Jul 15;33(14):2202-2204. doi: 10.1093/bioinformatics/btx153.

Authors

Gregory W Vurture¹, Fritz J Sedlazeck², Maria Nattestad¹, Charles J Underwood¹, Han Fang^{1

3}, James Gurtowski¹, Michael C Schatz^{1

2}

Affiliations

¹ Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
² Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
³ Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.

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 .

Contact: mschatz@jhu.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Animals
Computational Biology / methods*
Evolution, Molecular
Genome
Genome Size
Heterozygote
Internet
Sequence Analysis, DNA / methods*
Software*

Grants and funding

R01 HG006677/HG/NHGRI NIH HHS/United States