1Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium
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Summary:We have developed essaMEM, a tool for finding maximal exact matches that can be used in genome comparison and read mapping. essaMEM enhances an existing sparse suffix array implementation with a sparse child array. Tests indicate that the enhanced algorithm for finding maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain competitive with the more complex compressed suffix arrays.Availability:Source code is freely available at https://github.ugent.be/ComputationalBiology/essaMEM.Contact:Michael.Vyverman@UGent.beSupplementary information:Supplementary data are available at Bioinformatics online.