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PEMer

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

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PEMer classification

PEMer specifications

Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Input format:
FASTA
Programming languages:
Perl, Python
Stability:
Stable

PEMer distribution

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No versioning.

Credits

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Publications

Institution(s)

Gene Expression Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr, Heidelberg, Germany

Link to literature

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