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

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. :. . Unbiased Probabilistic Mapping of Next-Generation Sequencing Reads. Nathan Clement. Computational Sciences Laboratory. Brigham Young University. Provo, Utah, USA. Next-Generation Sequencing. Problem Statement . 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. Assembly, and Alignment Methods . Andy Nagar. Agenda. Background. Next Generation Sequencing. Sequence Assembly. Sequence Alignment. Traditional Alignment Algorithms. Next Generation Alignment Algorithms. Craig A. . Praul. Co- Director . Genomics Core Facility. Huck Institutes of the Life Sciences. Penn State University. A very short history of DNA sequencing. I started from the conviction that, if different DNA species exhibited . . 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. 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 . 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. 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 . 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. Next-generation sequencing technology. Outline. First generation sequencing. Next generation sequencing (current). AKA: . Second generation sequencing. Massively parallel sequencing. Ultra high-throughput sequencing. Analysis 2015. - RNA-sequencing . Jonas Andreas . Sibbesen. & Lasse Maretty. Bioinformatics Centre, University of Copenhagen . Bioinformatics Centre. Next Generation Sequencing Analysis 2015 - RNA-seq. Cynthia N Perry, PhD. Assistant Academic Dean of Admissions. Assistant Professor, Molecular Medicine. Department of Medical Education. Foster School of Medicine. https://. youtu.be. /KiQgrK3tge8. Genomics and Healthcare.