PPT-Introduction to Short Read Sequencing Analysis

James Knight with many slides adapted from Jim Noonan GENE 760 R ule to remember when using bioinformatics t ools Computer scientists and mathematiciansstatisticians make simplifications to speed up computations or to create a robust statistical model. Read Sequencing . Analysis. Jim Noonan. GENE 760. Sequence read lengths remain limiting. For most applications reads are . aligned. to a reference genome. Short reads contain inherently . limited information. Dr Gavin Band. Wellcome. Trust Advanced Courses; Genomic Epidemiology in Africa. , . 21. st. – 26. th. June 2015. Africa . Centre for Health and Population Studies, University of KwaZulu-Natal, Durban, South Africa. Jim Noonan. GENE 760. Sequence read lengths remain limiting. For most applications reads are . aligned. to a reference genome. Short reads contain inherently limited information. De novo . assembly of short reads is difficult. Jenny Wu. UCI Genomics High Throughput Facility. Outline. Goals : Practical guide to NGS data processing. Bioinformatics in NGS data analysis. Basics: terminology, data file formats, general workflow . Next Generation Sequencing. Hanlee Ji, M.D. . ã . Stanford University. Overview. Principles of next generation . DNA sequencing. Analysis of genetic variation and research applications. Ion . Mandoiu. Computer Science and Engineering Department. University of Connecticut. Outline. Background on high-throughput sequencing. Identification of tumor-specific . epitopes. Estimation of gene and . How we obtain the sequence of nucleotides of a species. …ACGTGACTGAGGACCGTG. CGACTGAGACTGACTGGGT. CTAGCTAGACTACGTTTTA. TATATATATACGTCGTCGT. ACTGATGACTAGATTACAG. ACTGATTTAGATACCTGAC. TGATTTTAAAAAAATATT…. Analysis 2015. - RNA-sequencing . Jonas Andreas . Sibbesen. & Lasse Maretty. Bioinformatics Centre, University of Copenhagen . Bioinformatics Centre. Next Generation Sequencing Analysis 2015 - RNA-seq. :. Computational Analysis of the Current State, Bottlenecks and Future Directions. Damla Senol. 1. , Jeremie Kim. 1,3. , Saugata Ghose. 1. , Can Alkan. 2. and Onur . Mutlu. 3,1. Nanopore Sequencing. Goals:. Introduce DNA Assembly and Alignment. Practice . rebuilding full sequences from reads. Sequencing by Synthesis Review. Modified PCR “builds” sequence over multiple cycles. Each strand of DNA is amplified into a cluster of identical DNA before sequencing. DNA Replication Review. Enzymes open . double stranded DNA. Origin of replication. Replication fork. DNA replication in 5’ to 3’ direction. Leading and Lagging Strands. RNA primers. DNA polymerase. Teeth are amazing -- the product of half a billion years of evolution. They provide fuel for the body by breaking apart other living things and they must do it again and again over a lifetime without breaking in the process. 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