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From: Adam P. <aph...@gm...> - 2014-02-06 16:12:33
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Hi Govinda, There is no minimum percent identity threshold for Nucmer and no guarantees on what it will find. Instead, the sensitivity and quality of the alignments depends on the minimum match size and cluster parameters chosen. The closest thing to an identity threshold are the dynamic programming extension scores, which are set to +3/-7. This equates to a min avg identity of 70% for the DP algorithm to continue extending. However, Nucmer will rarely find these low identity alignments, because they will likely not be seeded. With default parameters, Nucmer is generally sensitive to alignments >90% idy. If you want to cap the alignments to a certain identity, after the fact, you can run delta-filter with the -i option to filter alignments below your desired threshold. Hope this helps, -Adam On Tue, Feb 4, 2014 at 3:32 PM, Govinda Kamath <gk...@be...> wrote: > Hi, > > In NUCmer, what is the default percent identity threshold, above which > results are reported in the out.delta file? Also what is the metric (like > Hamming distance or Edit distance) is this calculated in? > > Thanks, > Govinda. > > > ------------------------------------------------------------------------------ > Managing the Performance of Cloud-Based Applications > Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. > Read the Whitepaper. > > http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > > |