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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: https://doi.org/10.1101/075978
Gregory W. Vurture
1Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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Fritz J. Sedlazeck
2Johns Hopkins University, Baltimore, 21218, MD, USA
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Maria Nattestad
1Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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Charles J. Underwood
1Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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Han Fang
1Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
3Stony Brook University, Stony Brook, 11794, NY, USA
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James Gurtowski
1Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
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Michael C. Schatz
1Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, NY, USA
2Johns Hopkins University, Baltimore, 21218, MD, USA
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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://qb.cshl.edu/genomescope/, https://github.com/schatzlab/genomescope.git

Contact mschatz@jhu.edu

Supplementary information Supplementary data are available at Bioinformatics online.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 19, 2016.
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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
bioRxiv 075978; doi: https://doi.org/10.1101/075978
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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
bioRxiv 075978; doi: https://doi.org/10.1101/075978

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