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PEMer title



PEMer package contains the computational codes and documentations for the algorithm developed to construct and analyze structural variants (SV) described in [1].

The package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from the ‘novel’ genome. Subsequent analysis with PEMer workflow on the simulated reads can facilitate parameterize PEMer workflow. BreakDB is a web accessible database developed to store, annotate and dsplay SV breakpoint events identified by PEMer and from other sources.

PEMer package can be downloaded from here.


[1] Korbel J, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein M: PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biology 2009, 10:R23.




Last updated 05/26/2009 by Xinmeng Jasmine Mu @ Gerstein lab, Yale University