Birol22052013

Référence

Birol, I., Raymond, A., Jackman, S.D., Pleasance, S., Coope, R., Taylor, G. A., Yuen, M.M.S, Keeling, C. I., Brand, D., Vandervalk, B. P., Kirk, H., Pandoh, P., Moore, R.A., Zhao, Y., Mungall, A. J., Jaquish, B., Yanchuk, A., Ritland, C., Boyle, B., Bousquet, J., Ritland, K., MacKay, J., Bohlmann, J. and Jones, S.J.M. (2013) Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics, 29(12):1492-1497. (URL )

Résumé

White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.Availability: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.Contact: ibirol@bcgsc.caSupplementary information: Supplementary data are available at Bioinformatics online.

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@ARTICLE { Birol22052013,
    AUTHOR = { Birol, I. and Raymond, A. and Jackman, S.D. and Pleasance, S. and Coope, R. and Taylor, G. A. and Yuen, M.M.S and Keeling, C. I. and Brand, D. and Vandervalk, B. P. and Kirk, H. and Pandoh, P. and Moore, R.A. and Zhao, Y. and Mungall, A. J. and Jaquish, B. and Yanchuk, A. and Ritland, C. and Boyle, B. and Bousquet, J. and Ritland, K. and MacKay, J. and Bohlmann, J. and Jones, S.J.M. },
    TITLE = { Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data },
    JOURNAL = { Bioinformatics },
    YEAR = { 2013 },
    VOLUME = { 29 },
    PAGES = { 1492--1497 },
    NUMBER = { 12 },
    ABSTRACT = { White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.Availability: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.Contact: ibirol@bcgsc.caSupplementary information: Supplementary data are available at Bioinformatics online. },
    DOI = { 10.1093/bioinformatics/btt178 },
    EPRINT = { http://bioinformatics.oxfordjournals.org/content/early/2013/05/03/bioinformatics.btt178.full.pdf+html },
    URL = { http://bioinformatics.oxfordjournals.org/content/early/2013/05/03/bioinformatics.btt178.abstract },
}

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