GenomeScope: fast reference-free genome profiling from short reads

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 ana...

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Bibliographic Details
Published in:	Bioinformatics (Oxford, England) Vol. 33; no. 14; pp. 2202 - 2204
Main Authors:	Vurture, Gregory W, Sedlazeck, Fritz J, Nattestad, Maria, Underwood, Charles J, Fang, Han, Gurtowski, James, Schatz, Michael C
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 15-07-2017
Subjects:	Animals Applications Notes Computational Biology - methods Evolution, Molecular Genome Genome Size Heterozygote Internet Sequence Analysis, DNA - methods Software
Online Access:	Get full text
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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. http://genomescope.org , https://github.com/schatzlab/genomescope.git . mschatz@jhu.edu. Supplementary data are available at Bioinformatics online.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
ISSN:	1367-4803 1367-4811
DOI:	10.1093/bioinformatics/btx153