essaMEM
Computational Tool
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General Information
DescriptionFinding maximal exact matches using enhanced sparse suffix arrays
Homepagehttps://github.ugent.be/ComputationalBiology/essaMEM
Publications
essaMEM: finding maximal exact matches using enhanced sparse suffix arrays
Michaël Vyverman; Bernard De Baets; Veerle Fack; Peter Dawyndt
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.be
Supplementary information: Supplementary data are available at Bioinformatics online.
DOI: https://doi.org/10.1093/bioinformatics/btt042
Metrics:
7
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