GenomeScope: fast reference-free genome profiling from short reads

被引：1246

作者：

Vurture, Gregory W. ^{[1
]}

Sedlazeck, Fritz J. ^{[2
,3
]}

Nattestad, Maria ^{[1
]}

Underwood, Charles J. ^{[1
]}

Fang, Han ^{[1
,4
]}

Gurtowski, James ^{[1
]}

Schatz, Michael C. ^{[1
,2
,3
]}

机构：

[1] Cold Spring Harbor Lab, Simons Ctr Quantitat Biol, POB 100, Cold Spring Harbor, NY 11724 USA

[2] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 USA

[3] Johns Hopkins Univ, Dept Biol, Baltimore, MD 21218 USA

[4] SUNY Stony Brook, Dept Appl Math & Stat, Stony Brook, NY 11794 USA

来源：

BIOINFORMATICS | 2017年 / 33卷 / 14期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

QUALITY;

D O I：

10.1093/bioinformatics/btx153

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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/genome scope. git. Contact: mschatz@ jhu. edu Supplementary information: Supplementary data are available at Bioinformatics online.

引用

页码：2202 / 2204

页数：3

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