GenomeScope: fast reference-free genome profiling from short reads.
| Autor: | Vurture GW; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Sedlazeck FJ; Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA., Nattestad M; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Underwood CJ; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Fang H; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA., Gurtowski J; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA., Schatz MC; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.; Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA. |
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| Jazyk: | angličtina |
| Zdroj: | Bioinformatics (Oxford, England) [Bioinformatics] 2017 Jul 15; Vol. 33 (14), pp. 2202-2204. |
| DOI: | 10.1093/bioinformatics/btx153 |
| Abstrakt: | 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. (© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com) |
| Databáze: | MEDLINE |
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