Abstract
Genome sequencing has achieved tremendous progress over the last few years. However, along with the speedup of the process and an ever increasing volume of data there are continuing concerns about the quality of the assembled sequence. Many genomes have been sequenced only to a draft, leaving the data in a series of more–or–less organized scaffolds, and many feature a small, but not negligible number of misassembled pieces. In this paper we present a new method for automated flagging of potential trouble spots in large assembled supercontigs. It can be incorporated into existing quality control pipelines and lead to a considerable improvement in the sensitivity to certain types of errors.
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References
Dunham, I., Shimizu, N., Roe, B., et al.: The DNA sequence of human chromosome 22. Nature 402, 489–495 (1999)
Hattori, M., Fujiyama, A., Taylor, T., et al.: The DNA sequence of human chromosome 21. Nature 405, 311–319 (2000)
Havlak, P., Chen, R., Durbin, K.J., Egan, A., Ren, Y., Song, X.-Z., Weinstock, G.M., Gibbs, R.A.: The Atlas genome assembly system. Genome Res. 14, 721–732 (2004)
Huang, X., Wang, J., Aluru, S., Yang, S.-P., Hillier, L.: PCAP: A wholegenome assembly program. Genome Res. 13, 2164–2170 (2003)
International Human Genome Mapping Consortium: A physical map of the human genome. Nature 409, 934–941 (2001)
International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001)
International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004)
Jaffe, D.B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J.P., Zody, M.C., Lander, E.S.: Whole–genome sequence assembly for mammalian genomes: Arachne2. Genome Res. 13, 91–96 (2003)
Kent, W.J., Haussler, D.: Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11, 1541–1548 (2001)
Mouse Genome Sequencing Consortium: Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002)
Mullikin, J., Ning, Z.: The Phusion assembler. Genome Res. 13, 81–90 (2003)
Rat Genome Sequencing Consortium: Genome sequence of the brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521 (2004)
Stojanovic, N., Chang, J.L., Lehoczky, J., Zody, M.C., Dewar, K.: Identification of mixups among DNA sequencing plates. Bioinformatics 18, 1418–1426 (2002)
Venter, J., Adams, M., Myers, E., et al.: The sequence of the human genome. Science 291, 1304–1351 (2001)
Weber, J.L., Myers, E.W.: Human whole–genome shotgun sequencing. Genome Res. 7, 401–409 (1997)
Xu, J., Gordon, J.I.: MapLinker: a software tool that aids physical map– linked whole genome shotgun assembly. Bioinformatics 21, 1265–1266 (2005)
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© 2006 Springer-Verlag Berlin Heidelberg
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Stojanovic, N. (2006). An Algorithm for the Automated Verification of DNA Supercontig Assemblies. In: Rothlauf, F., et al. Applications of Evolutionary Computing. EvoWorkshops 2006. Lecture Notes in Computer Science, vol 3907. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11732242_18
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DOI: https://doi.org/10.1007/11732242_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-33237-4
Online ISBN: 978-3-540-33238-1
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