Mobster: accurate detection of mobile element insertions in next generation sequencing data

被引：69

作者：

Djie Tjwan Thung ^{[1
]}

de Ligt, Joep ^{[1
,4
]}

Vissers, Lisenka E. M. ^{[1
]}

Steehouwer, Marloes ^{[1
]}

Kroon, Mark ^{[2
]}

de Vries, Petra ^{[1
]}

Slagboom, Eline P. ^{[2
]}

Ye, Kai ^{[3
]}

Veltman, Joris A. ^{[1
,5
]}

Hehir-Kwa, Jayne Y. ^{[1
]}

机构：

[1] RadboudUMC, Dept Human Genet, NL-6500 HB Nijmegen, Netherlands

[2] Leiden Univ, Med Ctr, Dept Mol Epidemiol, Leiden, Netherlands

[3] Washington Univ, Genome Inst, St Louis, MO USA

[4] KNAW, Hubrecht Inst, Utrecht, Netherlands

[5] Maastricht Univ, Med Ctr, Dept Clin Genet, Maastricht, Netherlands

来源：

GENOME BIOLOGY | 2014年 / 15卷 / 10期

基金：

欧洲研究理事会;

关键词：

HUMAN GENOME; STRUCTURAL VARIATION; L1; RETROTRANSPOSITION; ALU RETROTRANSPOSONS; DISEASE; LINE-1;

D O I：

10.1186/s13059-014-0488-x

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.

引用

页数：11

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