Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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An Optimized Strategy for Genome Assembly of Sanger/pyrosequencing Hybrid Data using Available Software

  • Jeong, Hae-Young (Laboratory of Microbial Genomics, Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Kim, Ji-Hyun F. (Field of Functional Genomics, School of Science, Korea University of Science and Technology (UST))
  • Published : 2008.06.30
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Abstract

During the last four years, the pyrosequencing-based 454 platform has rapidly displaced the traditional Sanger sequencing method due to its high throughput and cost effectiveness. Meanwhile, the Sanger sequencing methodology still provides the longest reads, and paired-end sequencing that is based on that chemistry offers an opportunity to ensure accurate assembly results. In this report, we describe an optimized approach for hybrid de novo genome assembly using pyrosequencing data and varying amounts of Sanger-type reads. 454 platform-derived contigs can be used as single non-breakable virtual reads or converted to simpler contigs that consist of editable, overlapping pseudoreads. These modified contigs maintain their integrity at the first jumpstarting assembly stage and are edited by fragmenting and rejoining. Pre-existing assembly software then can be applied for mixed assembly with 454-derived data and Sanger reads. An effective method for identifying genomic differences between reference and sample sequences in whole-genome resequencing procedures also is suggested.

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References

  1. Chaisson, M.J., and Pevzner, P.A. (2008). Short read fragment assembly of bacterial genomes. Genome Res. 18, 324-330. https://doi.org/10.1101/gr.7088808
  2. Goldberg, S.M., Johnson, J., Busam, D., Feldblyum, T., Ferriera, S., and Friedman, R., et al. (2006). A Sanger/pyrosequencing hybrid approach for the generation of highquality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. USA 103, 11240-11245 https://doi.org/10.1073/pnas.0604351103
  3. Huang, X., Wang, J., Aluru, S., Yang, S.P., and Hillier, L. (2003). PCAP: a whole-genome assembly program. Genome Res. 13, 2164-2170. https://doi.org/10.1101/gr.1390403
  4. Huson, D.H., Reinert, K., Kravitz, S.A., Remington, K.A., Delcher, A.L., Dew, I.M., et al. (2001). Design of a compartmentalized shotgun assembler for the human genome. Bioinformatics 17 Suppl 1, S132-139. https://doi.org/10.1093/bioinformatics/17.suppl_1.S132
  5. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380. https://doi.org/10.1038/nature03959
  6. Pop, M., and Kosack, D. (2004). Using the TIGR assembler in shotgun sequencing projects. Methods Mol. Biol. 255, 279-294.
  7. Shendure, J., Mitra, R.D., Varma, C., and Church, G.M. (2004). Advanced sequencing technologies: methods and goals. Nat. Rev. Genet. 5, 335-344.
  8. Sundquist, A., Ronaghi, M., Tang, H., Pevzner, P., and Batzoglou, S. (2007). Whole-genome sequencing and assembly with high-throughput, short-read technologies. PLoS ONE 2, e484. https://doi.org/10.1371/journal.pone.0000484

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