TY - JOUR 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. PY - 2009 DA - 2009/02/23 TI - PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data JO - Genome Biology SP - R23 VL - 10 IS - 2 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. SN - 1474-760X UR - https://doi.org/10.1186/gb-2009-10-2-r23 DO - 10.1186/gb-2009-10-2-r23 ID - Korbel2009 ER -