title: 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 contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes.
  
  
  CONCLUSIONS
  The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner.
authors.forename: Marten
authors.initials: M
authors.lastname: Boetzer
authors.affiliation: BaseClear B,V,, Genome analysis and technology department, Einsteinweg 5, Leiden 2333 CC, The Netherlands. walter.pirovano@baseclear.com.
authors.forename: Walter
authors.initials: W
authors.lastname: Pirovano
mesh_terms: D015723:Gene Library; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software