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

Utturkar, Sagar M.; Klingeman, Dawn Marie; Land, Miriam L.; Schadt, Christopher Warren; Doktycz, Mitchel John; Pelletier, Dale A.; Brown, Steven D.

doi:10.1093/bioinformatics/btu391

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

Journal Article · Sat Jun 14 00:00:00 EDT 2014 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btu391· OSTI ID:1149743

Utturkar, Sagar M. ^[1]; Klingeman, Dawn Marie ^[2]; Land, Miriam L. ^[2]; Schadt, Christopher Warren ^[3]; Doktycz, Mitchel John ^[3]; Pelletier, Dale A. ^[3]; Brown, Steven D. ^[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
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

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1149743

Journal Information:: Bioinformatics, Vol. 30, Issue 19; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 61 works

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