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Title: Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences

Our motivation with this work was to assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences. Our results show 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. As to availability and implementation–all assembly tools except CLC Genomics Workbench are freely available under GNU General Public License.
Authors:
 [1] ;  [2] ;  [2] ;  [3] ;  [3] ;  [3] ;  [3]
  1. Univ. of Tennessee, Knoxville, TN (United States). Graduate School of Genome Science and Technology
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)/ Biosciences Division
  3. Univ. of Tennessee, Knoxville, TN (United States). Graduate School of Genome Science and Technology; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)/ Biosciences Division
Publication Date:
OSTI Identifier:
1149743
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 30; Journal Issue: 19; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Research Org:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES PMI; draft genome assemblies