Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs

Background: Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In an earlier work, an O(n/p) time parallel algorithm has been given for this problem. Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating (n) messages ( being the size of the alphabet). Results: In this paper we present a (n/p) time parallel algo...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh, Matthew Vaughn, Vishal Thapar
• Keywords: Algorithms, Assembly Problem Fall, BMCBI 2010, Bruijn Graph