Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.

ABSTRACT: A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently. With recent improvements in DNA sequencing technologies, it is expected that the memory footprint required for the assembly process will increase dramatically and will emerge as a limiting factor in processing widely available NGS-generated reads. In this report, we compare current memory-efficient techniques for genome assembly with respect to quality, memory consumption and execution time. Our experiments prove that it is possible to generate draft assemblies of reasonable quality on conventional multi-purpose computers with very limited available memor

SUBMITTER: Kleftogiannis D 

PROVIDER: S-EPMC3785575 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature