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

Genome biology | Jan 19, 2009

http://www.ncbi.nlm.nih.gov/pubmed/19236709

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.

Pubmed ID: 19236709 RIS Download

Mesh terms: Base Sequence | Computational Biology | Computer Simulation | Genome | Genomic Structural Variation | Genomics | Internet | Models, Genetic | Software