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CGAL computing genome assembly likelihoods
RahmanandPachterGenomeBiology2013,14:R8
/2013/14/1/R8
METHOD
OpenAccess
CGAL:computinggenomeassemblylikelihoods
AtifRahman1andLiorPachter1,2*
Abstract
Assemblyalgorithmshavebeenextensivelybenchmarkedusingsimulateddatasothatresultscanbecomparedto
groundtruth.However,indenovoassembly,onlycrudemetricssuchascontignumberandsizearetypicallyused
toevaluateassemblyquality.WepresentCGAL,anovellikelihood-basedapproachtoassemblyassessmentinthe
absenceofagroundtruth.Weshowthatlikelihoodismoreaccuratethanothermetricscurrentlyusedfor
evaluatingassemblies,anddescribeitsapplicationtotheoptimizationandcompar
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