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

GenomeScope: fast reference-free genome profiling from short reads.

Author information

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.

PMID:
28369201
PMCID:
PMC5870704
DOI:
10.1093/bioinformatics/btx153
[Indexed for MEDLINE]
Free PMC Article

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