HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.

ABSTRACT:

Background

Current high-throughput sequencing technologies generate large numbers of relatively short and error-prone reads, making the de novo assembly problem challenging. Although high quality assemblies can be obtained by assembling multiple paired-end libraries with both short and long insert sizes, the latter are costly to generate. Recently, GAGE-B study showed that a remarkably good assembly quality can be obtained for bacterial genomes by state-of-the-art assemblers run on a single short-insert library with very high coverage.

Results

In this paper, we introduce a novel hierarchical genome assembly (HGA) methodology that takes further advantage of such very high coverage by independently assembling disjoint subsets of reads, combining assemblies of the subsets, and

SUBMITTER: Al-Okaily AA 

PROVIDER: S-EPMC4779561 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature