PPT-GNUMap : Unbiased Probabilistic Mapping of Next-Generation Sequencing Reads

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Nathan Clement Computational Sciences Laboratory Brigham Young University Provo Utah USA NextGeneration Sequencing Problem Statement Map nextgeneration sequence

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GNUMap : Unbiased Probabilistic Mapping of Next-Generation Sequencing Reads: Transcript

Nathan Clement Computational Sciences Laboratory Brigham Young University Provo Utah USA NextGeneration Sequencing Problem Statement Map nextgeneration sequence reads with variable nucleotide confidence to . . Krumlov. January 2012. Mapping and variant calling. from short read data. Gerton Lunter. Wellcome. Trust Centre for Human Genetics. Oxford. June 26, 2000: “G-Day”. Completion of the Working Draft of the Human Genome. : mapping massive amount of oligonucleotides to the genome. Hui. Jiang . et al.. Bioinformatics (2008) 24: 2395-2396. The . GNUMAP. algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. DNA Sequencing. Platforms:. Evolving Tools for . Cancer Research. Norma Neff. Bioengineering / Quake Lab. Sequencing Core Director. Stem Cell Institute. SIM1 G1115 / G0821. nfneff@stanford.edu. Emulsion PCR-based Sequencing Technologies. :. informatics & software aspects. Gabor T. Marth. Boston College Biology . Department. BI543 Fall 2013. January 29, 2013. Traditional DNA sequencing. Genetics of living organisms. DNA. Chromosomes. . Krumlov. January 2012. Mapping and variant calling. from short read data. Gerton Lunter. Wellcome. Trust Centre for Human Genetics. Oxford. June 26, 2000: “G-Day”. Completion of the Working Draft of the Human Genome. INTRODUCTION . The most commonly used technology until a few years ago – BAC. WHOLE GENOME SEQUENCING. ADVANTAGES OF WGS. Utility of next – gen sequence reads . The next-generation platforms are effecting a complete paradigm shift, not only in the organization of large-scale data production, but also in the downstream bioinformatics, IT, and LIMS support required for high data utility and correct interpretation.. Lenka Veselovská. Laboratory of Developmental Biology and Genomics . Next Generation Sequencing (NGS) . M. odern high-throughput DNA sequencing technologies. parallel, rapid . Decreasing price, time, workflow complexity, error rate. Hardison. Genomics . 3_2. 1. 1/20/14. Second generation sequencing. Michael . Metzker. review. (2010) Nature Reviews Genetics . 11. : 31-46. 1/20/14. 2. Two generations of sequencing technology. Feature. . Nearly . all modern DNA sequencing procedures require a concentrated amount of . single-stranded . DNA known as a . template. . A template is simply a piece of DNA of . sufficient . length and quality to allow for its sequencing (most sequencing methods . 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. David . Tse. . Dept. of EECS. U.C. Berkeley. LIDS Student Conference. MIT. Feb. 2, 2012. Research supported by NSF Center for Science of Information.. TexPoint fonts used in EMF: . A. A. A. A. A. A. and Accurate Assembly Polishing Algorithm. Can Firtina. 1. , Jeremie S. Kim. 1,2. , Mohammed Alser. 1. , . Damla. . Senol. Cali. 2. , A. . Ercument. Cicek. 3. ,. Can Alkan. 3. , and . Onur. Mutlu. the DNA sequencing?. DNA sequencing determines the order of the four chemical building blocks - called "bases" - that make up the DNA molecule. . The . sequence tells scientists the kind of genetic information that is carried in a particular DNA segment.

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