TY - JOUR AU - Kundeti, Vamsi K. AU - Rajasekaran, Sanguthevar AU - Dinh, Hieu AU - Vaughn, Matthew AU - Thapar, Vishal PY - 2010 DA - 2010/11/15 TI - Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs JO - BMC Bioinformatics SP - 560 VL - 11 IS - 1 AB - 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 Θ(n Σ) messages (Σ being the size of the alphabet). SN - 1471-2105 UR - https://doi.org/10.1186/1471-2105-11-560 DO - 10.1186/1471-2105-11-560 ID - Kundeti2010 ER -