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  • Ringman
    Junior Member
    • Sep 2013
    • 1
    #1

    mapping a consensus sequence

    Is there a suggested mapper and variant caller for mapping a consensus sequence (contigs) to a reference? Or is there a suggested method for doing this with mappers that don't support it. Currently we've been trying to use bowtie2 and have shredded contigs (with overlapping segments and 5x coverage) map with a reference, but the results are way too different from the results of mapping the reads against the reference.

    Any thoughts?
    Tags: None
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