Suffix Tree Contraction

ERA: Efficient Serial and Parallel Suffix Tree Construction​

We developed a disk-based suffix tree construction method, called Elastic Range (ERA), which works efficiently with very long strings that are much larger than the available memory. ERA partitions the tree construction process horizontally and vertically and minimizes I/Os by dynamically adjusting the horizontal partitions independently for each vertical partition, based on the evolving shape of the tree and the available memory. Where appropriate, ERA also groups vertical partitions together to amortize the I/O cost. We developed a serial version; a parallel version for shared-memory and shared-disk multi-core systems; and a parallel version for shared-nothing architectures. ERA indexes the entire human genome in 19 minutes on an ordinary desktop computer. For comparison, the fastest existing method needs 15 minutes using 1024 CPUs on an IBM BlueGene supercomputer.

Relevant Publications

Essam Mansour, Amin Allam, Spiros Skiadopoulos, Panos Kalnis: ERA: Efficient Serial and Parallel Suffix Tree Construction for Very Long Strings. PVLDB 5(1): 49-60 (2011)  (PDF) (BibTeX)