Irena Lanc

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The advent of new sequencing technologies has generated extremely large amounts of information. To successfully apply bioinformatics tools to such large datasets, they need to exhibit scalability and ideally elasticity in diverse computing environments. We describe the application of Weaver to the PEMer structural variation detection workflow. Because the(More)
ion Description Run(function, inputs) Apply inputs to function. Map(function, inputs) For each input in inputs, apply function. MapReduce(mapper, reducer, inputs) For each input in inputs apply mapper, sort intermediate outputs, and then apply reducer. AllPairs(function, inputs_a, inputs_b) Apply function to all combinations of inputs_a and inputs_b.(More)
The dramatic decrease in sequencing cost has led to an unprecedented number of new projects. Because finishing a genome often involves painstaking work, most sequencing efforts are satisfied by an initial draft assembly. Reliable analysis of synteny, gene expansion, and structural variation, however, is contingent upon the available draft being an accurate(More)
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