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  4. Repetitive DNA
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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.

Specifications

Software type:
Package
Interface:
Command line interface
Restrictions to use:
Academic users only
Input format:
FASTA
Operating system:
Unix/Linux
Programming languages:
Perl, Python
Computer skills:
Advanced
Stability:
Stable
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Publications

  • (Korbel et al., 2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome biology.
    PMID: 19236709

Classification

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