PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

被引：173

作者：

Korbel, Jan O. ^{[1
,2
,3
]}

Abyzov, Alexej ^{[3
]}

Mu, Xinmeng Jasmine ^{[4
]}

Carriero, Nicholas ^{[5
]}

Cayting, Philip ^{[3
]}

Zhang, Zhengdong ^{[3
]}

Snyder, Michael ^{[3
,4
]}

Gerstein, Mark B. ^{[3
,4
,5
,6
]}

机构：

[1] European Mol Biol Lab, Gene Express Unit, D-69117 Heidelberg, Germany

[2] EMBL EBI, EMBL Outstat Hinxton, Cambridge CB10 1SA, England

[3] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA

[4] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA

[5] Yale Univ, Dept Comp Sci, New Haven, CT 06511 USA

[6] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 02期

关键词：

COPY-NUMBER VARIATION; FINE-SCALE; RESOLUTION; IDENTIFICATION; TOOL; POLYMORPHISM; ELEMENTS; SNPS; MAP;

D O I：

10.1186/gb-2009-10-2-r23

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：

Personal-genomics endeavors, such as the 1000 Genomes project, are generating maps of genomic structural variants by analyzing ends of massively sequenced genome fragments. To process these we developed Paired-End Mapper (PEMer; http://sv.gersteinlab.org/pemer). This comprises an analysis pipeline, compatible with several next-generation sequencing platforms; simulation-based error models, yielding confidence-values for each structural variant; and a back-end database. The simulations demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors.

引用

页数：14

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