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
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 School of Biological Sciences > 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: | https://repository.cshl.edu/id/eprint/34472 |
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