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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-02

AUTHORS

Jan O Korbel, Alexej Abyzov, Xinmeng Jasmine Mu, Nicholas Carriero, Philip Cayting, Zhengdong Zhang, Michael Snyder, Mark B Gerstein

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. More... »

PAGES

r23

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/gb-2009-10-2-r23

    DOI

    http://dx.doi.org/10.1186/gb-2009-10-2-r23

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1048248560

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19236709


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