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:10.1093/bioinformatics/btx153

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

Whiting School of Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Pages (from-to)	2202-2204
Number of pages	3
Journal	Bioinformatics
Volume	33
Issue number	14
DOIs	https://doi.org/10.1093/bioinformatics/btx153
State	Published - Jul 15 2017

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btx153

Cite this

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abstract = "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.",

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AU - Vurture, Gregory W.

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AU - Nattestad, Maria

AU - Underwood, Charles J.

AU - Fang, Han

AU - Gurtowski, James

AU - Schatz, Michael C.

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AB - 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.

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GenomeScope: Fast reference-free genome profiling from short reads

Abstract

ASJC Scopus subject areas

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