Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies
Open accessAbstract
During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequence datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.
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Advanced next generation sequencing platforms such as Single Molecule Real-Time sequencing can be employed to reliably detect certain methylation signatures, as done for C. autoethanogenum.
“Advanced next generation sequencing platforms such as Single Molecule Real-Time (SMRT) sequencing can be employed to reliably detect certain methylation signatures (Flusberg et al., 2010; Fang et al., 2012) as it has been done for C. autoethanogenum (Utturkar et al., 2015).”
From Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks (2016) · cites this paper as Utturkar et al., 2015
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References 41 · Cited by 46
Research works printed but not linked: 1
- Ye C., Hill C., Koren S., Ruan J., Zhanshan M., Yorke J. A. & Zimin A. DBG2OLC: Efficient assembly of large genomes using the compressed overlap graph. Preprint at arXiv http://arxiv.org/abs/1410.2801 (2014). · arXiv
- Authors
- Utturkar, S. M., Klingeman, D. M., Bruno-Barcena, J. M., Chinn, M. S., Grunden, A. M., Köpke, M., & Brown, S. D.
- Affiliations
- University of Tennessee at Knoxville (US)
- Oak Ridge National Laboratory (US)
- North Carolina State University (US)
- Corresponding author
- Brown, Steven D
- Venue
- Scientific Data
- Published
- 2015-04-14
- Volume
- 2
- Issue
- 1
- Pages
- 150014-150014
- ISSN
- 2052-4463 (ISSN-L)
- PMC
- PMC4409012
- OpenAlex
- W2313765255
- Cited by
- 46
- References
- 41
- Citations by year
- 2025: 2 · 2024: 5 · 2023: 6 · 2022: 5 · 2021: 4 · 2020: 3 · 2019: 3 · 2018: 1 · 2017: 5 · 2016: 8 · 2015: 4
- Type
- data paper
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Scientific Data (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (AC05-00OR22725, DE--AC05--00OR22725, DE-AC05?, under Contract DE-AC05-00OR22725, 00OR22725)
- Battelle (DE-AC05- 00OR22725, AC05-00OR22725, DE-AC05)
- North Carolina Biotechnology Center
- North Carolina State University
- UT-Battelle (DE-AC05, DEAC05-00OR22725, Contract DE-AC05-00OR22725, AC05-00OR22725)
- Office of Science (DEAC05- 00OR22725, AC05-00OR22725)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK034987)
- Biological and Environmental Research (00OR22725, DE‐AC05–00OR22725)
- Oak Ridge National Laboratory (AC05-00OR22725, DE-AC05-00OR22725)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Physical Sciences › Engineering › Biomedical Engineering › Biofuel production and bioconversion
- Keywords
- Clostridium autoethanogenum, microbial genome assembly, long-read sequencing, PacBio long reads, next-generation sequencing, hybrid genome assembly, sequencing platform comparison
- MeSH terms
- Algorithms, Clostridium, Genome, Bacterial, Sequence Analysis, DNA, Genomics
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