AN OVERLAP DE NOVO METAGENOMICS GENE ASSEMBLER
A literature review about metagenomics assembly especially gene assemblers (peptide assemblers) the structure would be as follow Introduction : general introduction about assembly (definition – benefits – complexity …etc) . background: Mainly would give a brief background about bioinformatics and metagenomics so the none specialist reader will get a general idea. de novo assemblers Vs reference-based assemblers: Comparison between the two types of assemblers then we show the advantages of using de novo assemblers. Peptide assembly Vs nucleotide assembly : Comparison between the two types of assemblers and why here we could give a hint about why we will propose a peptide assembler. Overlap Graph vs de Bruijn Graph: Comparison between the two types of graphs and their use in the assembly process and why here we could give a hint about why we will an overlap graph review of peptide assemblers: a very brief review about reference-based peptide assemblers. detailed review about de novo peptide assemblers. both reviews should mention which graph type have been used in the papers. Papers : Yang, Y., & Yooseph, S. (2013). SPA: A short peptide assembler for metagenomic data. Nucleic Acids Research, 41(8). https://doi.org/10.1093/nar/gkt118 Y. W. Wu, M. Rho, T. G. Doak, and Y. Ye, “Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics,” Bioinformatics, vol. 28, no. 18, 2012. Y. Peng, H. C. M. Leung, S. M. Yiu, and F. Y. L. Chin, “IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth,” Bioinformatics, vol. 28, no. 11, pp. 1420–1428, Jun. 2012. T. Namiki, T. Hachiya, H. Tanaka, and Y. Sakakibara, “MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads,” Nucleic Acids Res., vol. 40, no. 20, pp. e155–e155, Nov. 2012. S. Boisvert, F. Raymond, É. Godzaridis, F. Laviolette, and J. Corbeil, “Ray Meta: scalable de novo metagenome assembly and profiling,” Genome Biol., vol. 13, no. 12, p. R122, Dec. 2012. R. Luo et al., “SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler,” Gigascience, vol. 1, no. 1, p. 18, Dec. 2012. B. Haider, T. H. Ahn, B. Bushnell, J. Chai, A. Copeland, and C. Pan, “Omega: An Overlap-graph de novo Assembler for Metagenomics,” Bioinformatics, vol. 30, no. 19, pp. 2717–2722, 2014. Y. Ye and H. Tang, “AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS,” J. Bioinform. Comput. Biol., vol. 7, no. 3, pp. 455–471, 2009. G. Peng, P. Ji, and F. Zhao, “A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes,” Genome Biol., vol. 17, no. 1, 2016. Zhang, Y., Sun, Y., & Cole, J. R. (2014). A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data. PLoS Computational Biology, 10(8), e1003737. Q. Wang et al., “Xander: employing a novel method for efficient gene-targeted metagenomic assembly,” Microbiome, vol. 3, no. 1, p. 32, 2015. D. Li, Y. Huang, C. M. Leung, R. Luo, H. F. Ting, and T. W. Lam, “MegaGTA: A sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs,” BMC Bioinformatics, vol. 18, pp. 5–8, 2017. I. Gregor, A. Schönhuth, and A. C. McHardy, “Snowball: Strain aware gene assembly of metagenomes,” in Bioinformatics, 2016, vol. 32, no. 17, pp. i649–i657. Liu, J., Lian, Q., Chen, Y., & Qi, J. (2019). Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads. Nucleic Acids Research, 47(5), 30.