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De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
Open accessAbstract
Novel high-throughput DNA sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. However, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. This study focuses on the Illumina sequencing platform that produces millions of very short sequences that are 35 bases in length. We propose a de novo assembler software that is dedicated to process such data. Based on a classical overlap graph representation and on the detection of potentially spurious reads, our software generates a set of accurate contigs of several kilobases that cover most of the bacterial genome. The assembly results were validated by comparing data sets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published genomes acquired by conventional sequencing of 1.5- to 3.0-kb fragments. We also provide indications that the broad coverage achieved by high-throughput sequencing might allow for the detection of clonal polymorphisms in the set of DNA molecules being sequenced.
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Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926
“…size of E. coli library (SRX000429); the other assemblers, including ABySS (Simpson et al. 2009), Velvet (Zerbino and Birney 2008), EULER-SR (Chaisson and Pevzner 2008), SSAKE (Warren et al. 2007), and Edena (Hernandez et al. 2008), have been evaluated using this data set (Simpson et al. 2009).”
MethodInfluentialFord, C. B., Lin, P. L., Chase, M. R., Shah, R. R., Iartchouk, O., Galagan, J., Mohaideen, N., Ioerger, T. R., Sacchettini, J. C., Lipsitch, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.811 · Cited by 437
Optimization of de novo transcriptome assembly from next-generation sequencing data
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Application of 'next-generation' sequencing technologies to microbial genetics
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293
De novo fragment assembly with short mate-paired reads: Does the read length matter?
Chaisson, M. J., Brinza, D., & Pevzner, P. A. (2009) · Genome Research · doi:10.1101/gr.079053.108 · Cited by 279
Zhang, W., Chen, J., Yang, Y., Tang, Y., Shang, J., & Shen, B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017915 · Cited by 250
De novo assembly of short sequence reads
Paszkiewicz, K., & Studholme, D. J. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq020 · Cited by 204
Tao, X., Gu, Y.-H., Wang, H.-Y., Zheng, W., Li, X., Zhao, C.-W., & Zhang, Y.-Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036234 · Cited by 168
Werth, B. J., Sakoulas, G., Rose, W. E., Pogliano, J., Tewhey, R., & Rybak, M. J. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01586-12 · Cited by 134
Comparative studies of de novo assembly tools for next-generation sequencing technologies
Lin, Y., Li, J., Shen, H., Zhang, L., Papasian, C. J., & Deng, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr319 · Cited by 126
Metadata
- Authors
- Hernandez, D., François, P., Farinelli, L., Østerås, M., & Schrenzel, J.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-03-10
- Volume
- 18
- Issue
- 5
- Pages
- 802-809
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2023911006
- Cited by
- 629
- References
- 1
- Type
- posted content
- Language
- en
- Open access
- bronze
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