Abstract
With the active sequencing studies, along with the advancement of the next-generation sequencing (NGS) technology, rapid progress has been made in genome analysis of various species. For the completion and analysis of the whole genome map, it is necessary to assemble the read results from NGS data for map completion. When reference models are available for assembly, similar sequences can be used for mapping assembly, whereas the de novo assembly method is applied when there are no models available. At this time, if the number of repeats in repeat regions is unclear, it would be challenging to assemble the whole genome map. Thus, the aim of this study was to conduct comparative analyses of the repeat regions using assemblies from various assembler tools automatically yielding repeat regions, and to carry out effective assembly analysis including repeat regions.
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References
Zerbino, D.R., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008)
Luo, R., et al.: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 18 (2012)
Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I.: ABySS: a parallel assembler for short read sequence data. Genome Res. 19(6), 1117–1123 (2009)
Chevreux, B., et al.: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14, 1147–1159 (2004)
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Pevzner, P.A.: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19(5), 455–477 (2012)
Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009)
Tempel, S.: Using and understanding RepeatMasker. Methods Mol. Biol. 859, 29–51 (2012)
Jurka, J.: Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 9, 418–420 (2000)
Smit, A.F.A., Hubley, R.: RepeatModeler Open-1.0 (2008–2015). http://www.repeatmasker.org
Bao, Z., Eddy, S.R.: Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269–1276 (2002)
Price, A.L., Jones, N.C., Pevzner, P.A.: De novo identification of repeat families in large genomes. In: Proceedings of the 13 Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2005) (2005, to appear)
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This work was supported by the Hongik University new faculty research support fund.
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Jung, J. (2017). The Comparative Analysis of the Repeat Regions from the Assembled Contigs. In: Park, J., Chen, SC., Raymond Choo, KK. (eds) Advanced Multimedia and Ubiquitous Engineering. FutureTech MUE 2017 2017. Lecture Notes in Electrical Engineering, vol 448. Springer, Singapore. https://doi.org/10.1007/978-981-10-5041-1_70
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DOI: https://doi.org/10.1007/978-981-10-5041-1_70
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