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The suffix tree is a data structure for indexing strings. It is used in avariety of applications such as bioinformatics, time series analysis,clustering, text editing and data compression. However, when the string and theresulting suffix tree are too large to fit into the main memory, most existingconstruction algorithms become very inefficient. This paper presents adisk-based suffix tree construction method, called Elastic Range (ERa), whichworks efficiently with very long strings that are much larger than theavailable memory. ERa partitions the tree construction process horizontally andvertically and minimizes I/Os by dynamically adjusting the horizontalpartitions independently for each vertical partition, based on the evolvingshape of the tree and the available memory. Where appropriate, ERa also groupsvertical partitions together to amortize the I/O cost. We developed a serialversion; a parallel version for shared-memory and shared-disk multi-coresystems; and a parallel version for shared-nothing architectures. ERa indexesthe entire human genome in 19 minutes on an ordinary desktop computer. Forcomparison, the fastest existing method needs 15 minutes using 1024 CPUs on anIBM BlueGene supercomputer.

ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings