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PMID: 24930142 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Validation Study

Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Bioinformatics (Oxford, England) ·Vol. 30 ·No. 19 ·2014-10-00 ·Pages 2709-16

Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD

Abstract

To assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences. 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. All assembly tools except CLC Genomics Workbench are freely available under GNU General Public License. [email protected] Supplementary data are available at Bioinformatics online.

MeSH Terms
Algorithms Base Sequence Computational Biology/methods Contig Mapping DNA, Bacterial/analysis DNA, Ribosomal/chemistry Genomics/methods Reproducibility of Results Sequence Analysis, DNA/methods
Chemicals
DNA, Bacterial DNA, Ribosomal
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Utturkar Sagar M
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.
Klingeman Dawn M
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.
Land Miriam L
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.
Schadt Christopher W
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.
Doktycz Mitchel J
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.
Pelletier Dale A
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.
Brown Steven D
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.
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Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
DOI
10.1093/bioinformatics/btu391
Published
2014-10-00
Epub
2014-00-14
Pages
2709-16
Language
English
Region
England
NLM ID
9808944
PMCID
PMC4173024
Subset
IM
External Links
PubMed source DOI: 10.1093/bioinformatics/btu391 PMC Full Text View journal details
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