GenomeScope: Fast reference-free genome profiling from short reads

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., Schatz, M. C. (July 2017) GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics, 33 (14). pp. 2202-2204. ISSN 1367-4803

URL: https://www.ncbi.nlm.nih.gov/pubmed/28369201
DOI: 10.1093/bioinformatics/btx153

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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:
Communities: CSHL labs > Schatz lab
Watson School > Publications
Depositing User: Matt Covey
Date: 15 July 2017
Date Deposited: 12 Apr 2017 16:10
Last Modified: 07 Jan 2019 19:42
PMCID: PMC5870704
Related URLs:
URI: http://repository.cshl.edu/id/eprint/34472

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