UMD Overlapper
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http://sourceforge.net/projects/umdoverlapper/files/umdoverlapper/initial%20release/umdoverlapper.tgz/download
ABOUT UMD Overlapper
UMD Overlapper takes a set of reads and quality data and determines which read pairs plausibly overlap; that is, it determines the pairs of reads containing subsequences that are similar enough that they may have come from overlapping parts of the genome.
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