Computing the burrows-wheeler transform of a string and its reverse
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Parallel suffix array and least common prefix for the GPU
Proceedings of the 18th ACM SIGPLAN symposium on Principles and practice of parallel programming
Computing the Burrows-Wheeler transform of a string and its reverse in parallel
Journal of Discrete Algorithms
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Summary: We introduce the tool mkESA, an open source program for constructing enhanced suffix arrays (ESAs), striving for low memory consumption, yet high practical speed. mkESA is a user-friendly program written in portable C99, based on a parallelized version of the Deep-Shallow suffix array construction algorithm, which is known for its high speed and small memory usage. The tool handles large FASTA files with multiple sequences, and computes suffix arrays and various additional tables, such as the LCP table (longest common prefix) or the inverse suffix array, from given sequence data. Availability: The source code of mkESA is freely available under the terms of the GNU General Public License (GPL) version 2 at http://bibiserv.techfak.uni-bielefeld.de/mkesa/. Contact: rhomann@techfak.uni-bielefeld.de