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  • annguyen
    replied
    I think those are default penalty weights:

    Gap open: cost to make gaps
    Gap extension: cost to make gaps bigger

    Leave a comment:


  • Victory
    started a topic gap penalty in BWA

    gap penalty in BWA

    Hi,
    I have short question about gap penalty in BWA. The manual said that the gap open penalty is 11 and gap extension penalty is 4. Does the first gap position will be charged 11 or 15?
    Thank you

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