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

Jan O. Korbel; Alexej Abyzov; Xinmeng Jasmine Mu; Nicholas Carriero; Philip Cayting; Zhengdong Zhang; Michael Snyder; Mark B. Gerstein

doi:10.1186/gb-2009-10-2-r23

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

Jan O. Korbel, Alexej Abyzov, Xinmeng Jasmine Mu, Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark B. Gerstein

Research output: Contribution to journal › Article › peer-review

201 Scopus citations

Abstract

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.

Original language	English (US)
Article number	R23
Journal	Genome biology
Volume	10
Issue number	2
DOIs	https://doi.org/10.1186/gb-2009-10-2-r23
State	Published - Feb 23 2009
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2009-10-2-r23

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title = "PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data",

abstract = "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.",

author = "Korbel, {Jan O.} and Alexej Abyzov and Mu, {Xinmeng Jasmine} and Nicholas Carriero and Philip Cayting and Zhengdong Zhang and Michael Snyder and Gerstein, {Mark B.}",

note = "Funding Information: Funding was provided, in part, by the EU sixth framework programme (JOK) and by the Yale Center of Excellence in Genomic Science grant provided by the NIH (AA, XM, NC, PC, ZZ, MS, and MBG). We thank other members of the 1000 Genomes project [47] for valuable discussions and for sharing data sets. Furthermore, we thank the Yale High Performance Computation Center (funded by NIH grant: RR19895-02) for technical support.",

year = "2009",

month = feb,

day = "23",

doi = "10.1186/gb-2009-10-2-r23",

language = "English (US)",

volume = "10",

journal = "Genome biology",

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publisher = "BioMed Central",

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T2 - A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

AU - Korbel, Jan O.

AU - Abyzov, Alexej

AU - Mu, Xinmeng Jasmine

AU - Carriero, Nicholas

AU - Cayting, Philip

AU - Zhang, Zhengdong

AU - Snyder, Michael

AU - Gerstein, Mark B.

N1 - Funding Information: Funding was provided, in part, by the EU sixth framework programme (JOK) and by the Yale Center of Excellence in Genomic Science grant provided by the NIH (AA, XM, NC, PC, ZZ, MS, and MBG). We thank other members of the 1000 Genomes project [47] for valuable discussions and for sharing data sets. Furthermore, we thank the Yale High Performance Computation Center (funded by NIH grant: RR19895-02) for technical support.

PY - 2009/2/23

Y1 - 2009/2/23

N2 - 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.

AB - 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.

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

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