Efficient parallel construction of suffix trees for genomes larger than main memory

Abstract

The construction of suffix tree for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become everyday more complex, requiring fast queries to multiple genomes. In this paper we presented Parallel Continuous Flow PCF, a parallel suffix tree construction method that is suitable for very long strings. We tested our method on the construction of suffix tree of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input string grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the Human genome in 7 minutes using 172 nodes.