title: Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.
abstract: BACKGROUND
  To assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences.
  
  
  RESULTS
  Illumina, 454 and PacBio sequencing technologies were used to generate de novo and hybrid genome assemblies for four different bacteria, which were assessed for quality using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools. Differences in predictions of multiple copies of rDNA operons for each respective bacterium were evaluated by PCR and Sanger sequencing, and then the validated results were applied as an additional criterion to rank assemblies. In general, assemblies using longer PacBio reads were better able to resolve repetitive regions. In this study, the combination of Illumina and PacBio sequence data assembled through the ALLPATHS-LG algorithm gave the best summary statistics and most accurate rDNA operon number predictions. This study will aid others looking to improve existing draft genome assemblies.
  
  
  METHODS
  All assembly tools except CLC Genomics Workbench are freely available under GNU General Public License.
  
  
  BACKGROUND
  brownsd@ornl.gov
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Sagar M
authors.initials: SM
authors.lastname: Utturkar
authors.affiliation: Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Klingeman
authors.affiliation: Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Miriam L
authors.initials: ML
authors.lastname: Land
authors.affiliation: Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Schadt
authors.affiliation: Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Mitchel J
authors.initials: MJ
authors.lastname: Doktycz
authors.affiliation: Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Dale A
authors.initials: DA
authors.lastname: Pelletier
authors.affiliation: Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37919, USA and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000737:chemistry; D023281:Genomics / Q000379:methods*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal