Parallelized short read assembly of large genomes using de Bruijn graphs.

ABSTRACT:

Background

Next-generation sequencing technologies have given rise to the explosive increase in DNA sequencing throughput, and have promoted the recent development of de novo short read assemblers. However, existing assemblers require high execution times and a large amount of compute resources to assemble large genomes from quantities of short reads.

Results

We present PASHA, a parallelized short read assembler using de Bruijn graphs, which takes advantage of hybrid computing architectures consisting of both shared-memory multi-core CPUs and distributed-memory compute clusters to gain efficiency and scalability. Evaluation using three small-scale real paired-end datasets shows that PASHA is able to produce more contiguous high-quality assemblies in shorter time compared to

SUBMITTER: Liu Y 

PROVIDER: S-EPMC3167803 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature