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Making the difference: integrating structural variation detection tools.

Ke Lin, Sandra Smit, Guusje Bonnema

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    |December 16, 2014
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    Summary
    This summary is machine-generated.

    Structural variations in genomes drive evolution and speciation. This review surveys computational callers and integrated pipelines for detecting these variations, offering recommendations for population genomics studies.

    Keywords:
    integrative pipelinesnext generation sequencingpopulation genomicsstructural variation detection

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    Area of Science:

    • Genomics
    • Bioinformatics
    • Evolutionary Biology

    Background:

    • Phenotypic variation, adaptation, and speciation are linked to genomic structural variations across all life forms.
    • Next-generation sequencing has spurred the development of numerous computational algorithms (callers) for detecting structural variations.

    Purpose of the Study:

    • To review existing structural variation callers.
    • To discuss challenges in integrating different callers into pipelines.
    • To survey pipelines used in population genomics and provide recommendations.

    Main Methods:

    • Review of computational callers utilizing split-read and paired-end mapping.
    • Analysis of integrated pipelines for population genomics.
    • Identification of challenges in structural variation detection and pipeline construction.

    Main Results:

    • No single caller is a community standard; integrated pipelines are increasingly used.
    • Different callers excel at detecting specific types of structural variations.
    • Recommendations for setting up structural variation detection pipelines are provided.

    Conclusions:

    • Integrated pipelines are essential for comprehensive structural variation detection.
    • Careful selection and combination of callers are crucial for population genomics studies.
    • Future research should address remaining challenges in structural variation detection.