Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences
Abstract
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:
-
- 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
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1149743
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Volume: 30; Journal Issue: 19; Journal ID: ISSN 1367-4803
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; PMI; draft genome assemblies
Citation Formats
Utturkar, Sagar M., Klingeman, Dawn Marie, Land, Miriam L., Schadt, Christopher Warren, Doktycz, Mitchel John, Pelletier, Dale A., and Brown, Steven D. Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences. United States: N. p., 2014.
Web. doi:10.1093/bioinformatics/btu391.
Utturkar, Sagar M., Klingeman, Dawn Marie, Land, Miriam L., Schadt, Christopher Warren, Doktycz, Mitchel John, Pelletier, Dale A., & Brown, Steven D. Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences. United States. https://doi.org/10.1093/bioinformatics/btu391
Utturkar, Sagar M., Klingeman, Dawn Marie, Land, Miriam L., Schadt, Christopher Warren, Doktycz, Mitchel John, Pelletier, Dale A., and Brown, Steven D. Sat .
"Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences". United States. https://doi.org/10.1093/bioinformatics/btu391. https://www.osti.gov/servlets/purl/1149743.
@article{osti_1149743,
title = {Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences},
author = {Utturkar, Sagar M. and Klingeman, Dawn Marie and Land, Miriam L. and Schadt, Christopher Warren and Doktycz, Mitchel John and Pelletier, Dale A. and Brown, Steven D.},
abstractNote = {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.},
doi = {10.1093/bioinformatics/btu391},
journal = {Bioinformatics},
number = 19,
volume = 30,
place = {United States},
year = {Sat Jun 14 00:00:00 EDT 2014},
month = {Sat Jun 14 00:00:00 EDT 2014}
}
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Cited by: 61 works
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Table 1: Summary of sequence data coverage
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Draft Genome Sequence of Thalassotalea sp. Strain ND16A Isolated from Eastern Mediterranean Sea Water Collected from a Depth of 1,055 Meters
journal, November 2014
- Stelling, S. C.; Techtmann, S. M.; Utturkar, S. M.
- Genome Announcements, Vol. 2, Issue 6
Draft Genome Sequences of Four Streptomyces Isolates from the Populus trichocarpa Root Endosphere and Rhizosphere
journal, December 2015
- Klingeman, Dawn M.; Utturkar, Sagar; Lu, Tse-Yuan S.
- Genome Announcements, Vol. 3, Issue 6
Linked read technology for assembling large complex and polyploid genomes
journal, September 2018
- Ott, Alina; Schnable, James C.; Yeh, Cheng-Ting
- BMC Genomics, Vol. 19, Issue 1
Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer
journal, January 2016
- Benítez-Páez, Alfonso; Portune, Kevin J.; Sanz, Yolanda
- GigaScience, Vol. 5, Issue 1
Transcriptomic Analysis of the Anterior Silk Gland in the Domestic Silkworm (Bombyx mori) – Insight into the Mechanism of Silk Formation and Spinning
journal, September 2015
- Chang, Huaipu; Cheng, Tingcai; Wu, Yuqian
- PLOS ONE, Vol. 10, Issue 9
Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches
journal, December 2015
- Lin, Hsin-Hung; Liao, Yu-Chieh
- PLOS ONE, Vol. 10, Issue 12
In Silico Whole Genome Sequencer and Analyzer (iWGS): a Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies
journal, September 2016
- Zhou, Xiaofan; Peris, David; Kominek, Jacek
- G3: Genes|Genomes|Genetics, Vol. 6, Issue 11
Colwellia psychrerythraea Strains from Distant Deep Sea Basins Show Adaptation to Local Conditions
journal, May 2016
- Techtmann, Stephen M.; Fitzgerald, Kathleen S.; Stelling, Savannah C.
- Frontiers in Environmental Science, Vol. 4
Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment
journal, October 2015
- Timm, Collin M.; Campbell, Alisha G.; Utturkar, Sagar M.
- Frontiers in Microbiology, Vol. 6
A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies
journal, July 2017
- Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Richard A.
- Frontiers in Microbiology, Vol. 8
Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System
journal, April 2016
- Timm, Collin M.; Pelletier, Dale A.; Jawdy, Sara S.
- Frontiers in Plant Science, Vol. 7
Coagulase-Negative Staphylococci Pathogenomics
journal, March 2019
- Argemi, Xavier; Hansmann, Yves; Prola, Kevin
- International Journal of Molecular Sciences, Vol. 20, Issue 5
Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine
journal, April 2016
- Xiao, Wenming; Wu, Leihong; Yavas, Gokhan
- Pharmaceutics, Vol. 8, Issue 2
Improving ancient DNA genome assembly
posted_content, August 2016
- Seitz, Alexander; Nieselt, Kay
- PeerJ Preprints
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