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  • Can Bowite2 do ungapped local alignments without mismatches?

    Hello,

    I am trying to make use of --local mode of Bowtie2, and I am looking for best possible alignments without gaps and mismatches.

    There seem to be no option that explicitly controls the number of mismatches and gaps along the whole length of alignments, only for the seed of alignments one can specify a maximum number of mismatches.

    To avoid having any gaps and mismatches outside of the seed, I attempted setting very high penalty for gaps and mismatches:

    bowtie2 --ignore-quals --local --mp 100,100 --rfg 100,100 -D 5 -R 1 -N 0 -L 20 -i S,1,2.00

    Nevertheless, I still get gapped alignments.

    I also don't of a way how I could make bowtie2 not to output any alignments for reads that have more than one alignment (i.e. there seem to be no equivalent of -m option in bowtie1).

    If someone has experience with configuring bowtie2 and could give an advice, that would be very appreciated.

    thanks,
    Sergei
    "Let’s start with the three fundamental Rules of Robotics...."

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