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| ==''' Team 1 Genome Assembly '''==
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| === In-Class Presentations ===
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| [[File: Team_1_Genome_Assembly_Presentation_1.pdf]]
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| === Genome Assembly Pipeline ===
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| [[File:workflow.png|border]]
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| === Our Goals ===
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| 1. To perform quality control on reads before and after assembling the genome.
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| 2. To evaluate the performance of assembly tools:
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| * Abyss
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| * ALLPATHS-LG
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| * SPADES
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| * SKESA
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| * Velvet
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| 3. To use the best 2 to perform de novo assembly based on the 50 isolates.
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| 4. To send off the highest quality result to gene prediction.
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| === References ===
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| Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler, QUAST: quality assessment tool for genome assemblies, Bioinformatics, Volume 29, Issue 8,
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| 15 April 2013, Pages 1072–1075, https://doi.org/10.1093/bioinformatics/btt086
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| Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol.
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| 2012;19(5):455–477. doi:10.1089/cmb.2012.0021
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| Butler, Jonathan et al. “ALLPATHS: de novo assembly of whole-genome shotgun microreads.” Genome research vol. 18,5 (2008): 810-20.
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| doi:10.1101/gr.7337908
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| Earl, Dent et al. “Assemblathon 1: a competitive assessment of de novo short read assembly methods.” Genome research vol. 21,12 (2011): 2224-41.
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| doi:10.1101/gr.126599.111
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| Maccallum, Iain et al. “ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.” Genome biology vol. 10,10 (2009):
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| R103. doi:10.1186/gb-2009-10-10-r103
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| Miller, Jason R et al. “Assembly algorithms for next-generation sequencing data.” Genomics vol. 95,6 (2010): 315-27. doi:10.1016/j.ygeno.2010.03.001
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| Pritt, J., Chen, N. & Langmead, B. FORGe: prioritizing variants for graph genomes. Genome Biol 19, 220 (2018). https://doi.org/10.1186/s13059-018-1595-x
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| Quainoo, S., Coolen, J.P., Hijum, S.A., Huynen, M.A., Melchers, W.J., Schaik, W.V., & Wertheim, H.F. (2017). Whole-Genome Sequencing of Bacterial Pathogens:
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| the Future of Nosocomial Outbreak Analysis. Clinical microbiology reviews, 30 4, 1015-1063 .
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| Rahman, A., Pachter, L. CGAL: computing genome assembly likelihoods. Genome Biol 14, R8 (2013). https://doi.org/10.1186/gb-2013-14-1-r8
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| Salzberg, Steven L et al. “GAGE: A critical evaluation of genome assemblies and assembly algorithms.” Genome research vol. 22,3 (2012): 557-67.
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| doi:10.1101/gr.131383.111
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| Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages
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| i884–i890, https://doi.org/10.1093/bioinformatics/bty560
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| Sohn, Jang-il; Nam, Jin-Wu. “The present and future of de novo whole-genome assembly”, Briefings in Bioinformatics, Vol 19.1 (2018).
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| doi.org/10.1093/bib/bbw096
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| Souvorov A., Agarwala R., & Lipman D.J. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology. 2018; 19(1).
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| doi:10.1186/s13059-018-1540-z
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| Tanja Magoc, Stephan Pabinger, Stefan Canzar, Xinyue Liu, Qi Su, Daniela Puiu, Luke J. Tallon, Steven L. Salzberg, GAGE-B: an evaluation of genome assemblers
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| for bacterial organisms, Bioinformatics, Volume 29, Issue 14, 15 July 2013, Pages 1718–1725, https://doi.org/10.1093/bioinformatics/btt273
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| Zerbino, D., & Birney, E. (n.d.). Velvet: de novo assembly using very short reads. Hinxton: European Bioinformatics Institute.
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