PPT-Bacterial Genome Assembly

Chris Fields Genome Assembly Saba Ghaffari 2020 1 PowerPoint by Saba Ghaffari Introduction Exercise Perform a bacterial genome assembly using PacBio HiFi data Evaluation and comparison of different datasets and parameters. Denovo genome Denovo genome outline outline novogenome from contigs from assembled contigs annotation Denovo genome Denovo genome Reads contig Gene Gene Annotation Gene Annotation Forgene sequencing . for . identification,. detection, . and control of . Bactrocera dorsalis (. Hendel. ). and other Tephritid pests. Thomas Walk, Scott . Geib. USDA-ARS Pacific Basin Agricultural Research Center, Hilo HI. Abhiram. Ranade. IIT Bombay. Genome. Constituent of living cells that determines hereditary characteristics a.k.a. DNA. Sequence of . nucleobases. : . A. denine, . G. uanine, . T. hymine, . C. ytosine. Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . School of Engineering. Assembler. Reference. Abyss 1.5.1. Simpson et al., J. T., Wong, K., Jackman, S. D., Schein, J. E., Jones,. . S. J., and . Birol. , I. (2009). Abyss: a parallel assembler for. . From Swab to Publication. Madison I. Dunitz. 1. , David A. Coil. 1. , Jenna M. Lang. 1. , Guillaume Jospin. 1. , Aaron E. Darling. 2. , Jonathan A. Eisen. 1. UC Davis Genome Center. 1. University of California, Davis; . By Kevin Chen, . Lior. . Pachter. PLoS. Computational Biology, 2005. David Kelley. State of . metagenomics. In July 2005, 9 projects had been completed.. General challenges were becoming apparent. Paper focuses on computational problems. Venter et. al (2004). Presented by. Ken . Vittayarukskul. Steven S. White.. Context of the Problem . Evolutionary history is directly tied to microbial genetics. Little is known. Until recently, microbial diversity was measured by PCR amplification and sequencing of only ribosomal genes. C. onifer . G. enome, Loblolly Pine. Jill Wegrzyn. Pieter . de Jong, . Chuck Langley, Dorrie Main, Keithanne Mockaitis, . Steven Salzberg, . Kristian. . Stevens. , Nick . Wheeler, Jim . Yorke, . Aleksey . Kerstin Lindblad-Toh1 et al.. Presentation by:. Keara Flores. Gustavo Diaz Cruz. Background. Human genome sequenced in 2003 and researchers learned 1.5% of it codes proteins. . 2005 Lindblad-Toh and colleagues begin effort to sequence domestic dog producing a SNP map allows for comparative analysis of the mammalian genome. genome . assembly. Sorin. . Istrail. CSCI1820 Short-read genome assembly algorithms. 3/6/2014. 1. Genomathica Assembler. Mathematica. notebook for genome assembly simulation. Assembler can be found at: . Christopher Desjardins, Ph.D.. Earl Lab. Broad Institute. Outline. Genomics Terminology. Assemblies vs. Variants. Assembly-based analyses. Orthology. Variant-based analyses. How to choose?. Basic Genomics Terminology. Genome: the total number of genes in an individual.. Human Genome- approx. 20,000 genes on the 46 human chromosomes.. Human Genome Project (HGP). Ongoing effort to completely map and sequence our genome.. j.abbott@dundee.ac.uk. What is assembly?. Assembly approaches. Short-read assembly. Long-read assembly. Hybrid assembly. Validation. Annotation. Overview. From your home directory, run the following command:.