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  • bfast localalign -U option?

    Hello,

    What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of concern?

  • #2
    Originally posted by Protaeus View Post
    Hello,

    What are the downsides of using the -U option at the bfast localalign step? I presume it'll be more computationally expensive, but are there things with the resulting data that would be of concern?
    When not using the '-U', bfast enforces that where the seeds/masks match the reference during 'bfast match' also match the reference in the final alignment. This is a constrained Smith Waterman alignment, which speeds up the local alignment. Using the '-U' option ignores those constraints.

    The philosophical question that the '-U' option lets one ask is if we get to a 100bp window in a 3Gb genome, should we constrain the alignment based on how we got there?

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    • #3
      That brings up a separate but related question I had. A lot of my recent illumina runs have been 101bp on bacterial genomes. Generally speaking, the key width for my indexes is 30. Would there be any reason to believe I would benefit from trying a larger key width? Or is this where the -U option in localalign might be helpful?

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