HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly.

ABSTRACT:

Background

The rapid advancement of sequencing technologies has made it possible to regularly produce millions of high-quality reads from the DNA samples in the sequencing laboratories. To this end, the de Bruijn graph is a popular data structure in the genome assembly literature for efficient representation and processing of data. Due to the number of nodes in a de Bruijn graph, the main barrier here is the memory and runtime. Therefore, this area has received significant attention in contemporary literature.

Results

In this paper, we present an approach called HaVec that attempts to achieve a balance between the memory consumption and the running time. HaVec uses a hash table along with an auxiliary vector data structure to store the de Bruijn graph thereby improvin

SUBMITTER: Rahman MM 

PROVIDER: S-EPMC5591975 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature