SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.

ABSTRACT:

Background

The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data.

Results

Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contig

SUBMITTER: Boetzer M 

PROVIDER: S-EPMC4076250 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature