The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Short read fragment assembly of bacterial genomes
Open accessAbstract
In the last year, high-throughput sequencing technologies have progressed from proof-of-concept to production quality. While these methods produce high-quality reads, they have yet to produce reads comparable in length to Sanger-based sequencing. Current fragment assembly algorithms have been implemented and optimized for mate-paired Sanger-based reads, and thus do not perform well on short reads produced by short read technologies. We present a new Eulerian assembler that generates nearly optimal short read assemblies of bacterial genomes and describe an approach to assemble reads in the case of the popular hybrid protocol when short and long Sanger-based reads are combined.
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Citations
Cites
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis
Andries, K., Verhasselt, P., Guillemont, J., Göhlmann, H. W. H., Neefs, J.-M., Winkler, H., Van Gestel, J., Timmerman, P., Zhu, M., Lee, E., et al. (2005) · Science · doi:10.1126/science.1106753 · Cited by 2,191 · cited 1×
“The applications of HTSR sequencing have been largely limited, albeit with great success, to resequencing (Andries et al. 2005), gene expression (Kim et al.”
BackgroundEdmonds, J. (1967) · Journal of Research of the National Bureau of Standards Section B Mathematics and Mathematical Physics · doi:10.6028/jres.071b.032 · Cited by 731
Cited by
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
De novo assembly of human genomes with massively parallel short read sequencing
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
“A few short read assemblers, including Velvet (Zerbino and Birney 2008), ALLPATHS (Butler et al. 2008), and EULER-SR (Chaisson and Pevzner 2008), have adopted this algorithm, explicitly or implicitly, and have been implemented and shown very promising performances.”
MethodInfluentialHow to apply de Bruijn graphs to genome assembly
Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011) · Nature Biotechnology · doi:10.1038/nbt.2023 · Cited by 673
Self-citationOptimization of de novo transcriptome assembly from next-generation sequencing data
Surget-Groba, Y., & Montoya-Burgos, J. I. (2010) · Genome Research · doi:10.1101/gr.103846.109 · Cited by 339
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
Metadata
- Authors
- Chaisson, M. J., & Pevzner, P. A.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-12-14
- Volume
- 18
- Issue
- 2
- Pages
- 324-330
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2151017710
- Cited by
- 441
- References
- 4
- Type
- posted content
- Language
- en
- Open access
- bronze
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