Dataset Information
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.
Ontology highlight
ABSTRACT: Motivation
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.Availability and implementation
All assembly tools except CLC Genomics Workbench are freely available under GNU General Public License.Contact
brownsd@ornl.govSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Utturkar SM
PROVIDER: S-EPMC4173024 | biostudies-literature | 2014 Oct
REPOSITORIES: biostudies-literature
Publications
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.
Bioinformatics (Oxford, England) 20140614 19
<h4>Motivation</h4>To assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences.<h4>Results</h4>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 ...[more]
