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GenomeScope: fast reference-free genome profiling from short reads.

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.

SUBMITTER: Vurture GW

PROVIDER: S-EPMC5870704 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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GenomeScope: fast reference-free genome profiling from short reads.

Vurture Gregory W GW Sedlazeck Fritz J FJ Nattestad Maria M Underwood Charles J CJ Fang Han H Gurtowski James J Schatz Michael C MC

Bioinformatics (Oxford, England) 20170701 14

<h4>Summary</h4>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.<h4>Availability and implementation</h ...[more]

PMID: 28369201

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