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.
authors.affiliation: Gene Expression Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr, Heidelberg, 69117, Germany. korbel@embl.de
authors.forename: Jan O
authors.initials: JO
authors.lastname: Korbel
authors.forename: Alexej
authors.initials: A
authors.lastname: Abyzov
authors.forename: Xinmeng Jasmine
authors.initials: XJ
authors.lastname: Mu
authors.forename: Nicholas
authors.initials: N
authors.lastname: Carriero
authors.forename: Philip
authors.initials: P
authors.lastname: Cayting
authors.forename: Zhengdong
authors.initials: Z
authors.lastname: Zhang
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Mark B
authors.initials: MB
authors.lastname: Gerstein
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016678:Genome; D056914:Genomic Structural Variation; D023281:Genomics / Q000379:methods; D020407:Internet; D008957:Models, Genetic; D012984:Software