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

@article{korbel:pemer, 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 Abyzov, Alexej and Mu, Xinmeng J. and Carriero, Nicholas and Cayting, Philip and Zhang, Zhengdong and Snyder, Michael and Gerstein, Mark B.}, citeulike-article-id = {4089107}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2009-10-2-r23}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19236709}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19236709}, day = {23}, doi = {10.1186/gb-2009-10-2-r23}, issn = {1465-6906}, journal = {Genome Biology}, keywords = {end, paired, structural, thesis, variation}, month = {February}, number = {2}, pages = {R23+}, posted-at = {2009-05-14 20:25:01}, priority = {2}, title = {PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data}, url = {http://dx.doi.org/10.1186/gb-2009-10-2-r23}, volume = {10}, year = {2009} }

TY - JOUR ID - korbel:pemer L3 - citeulike-article-id:4089107 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. IS - 2 JF - Genome Biology SN - 1465-6906 TI - PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data VL - 10 SP - R23 KW - end KW - paired KW - structural KW - thesis KW - variation AU - Korbel, Jan AU - Abyzov, Alexej AU - Mu, Xinmeng AU - Carriero, Nicholas AU - Cayting, Philip AU - Zhang, Zhengdong AU - Snyder, Michael AU - Gerstein, Mark PY - 2009/02/23/ UR - http://dx.doi.org/10.1186/gb-2009-10-2-r23 ER -