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.
PEMer : A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. / Korbel, Jan O.; Abyzov, Alexej; Mu, Xinmeng Jasmine; Carriero, Nicholas; Cayting, Philip; Zhang, Zhengdong; Snyder, Michael; Gerstein, Mark B.In: Genome biology, Vol. 10, No. 2, R23, 23.02.2009.
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