'Genome assembly' presentation slideshows

RNA Sequencing and transcriptome reconstruction Manfred G. Grabherr

RNA Sequencing and transcriptome reconstruction Manfred G. Grabherr. A historic perspective. Traditional: sequence cDNA libraries by Sanger Tens of thousands of pairs at most (20K genes in mammal) Redundancy due to highly expressed genes Not only coding genes are transcribed

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Genomic sequencing and its data analysis

Genomic sequencing and its data analysis. Dong Xu Digital Biology Laboratory Computer Science Department Christopher S. Life Sciences Center University of Missouri, Columbia E-mail: xudong@missouri.edu http://digbio.missouri.edu. Lecture Outline. Introduction to sequencing

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Introduction to Work Queue Applications

Introduction to Work Queue Applications. Applied Cyberinfrastructure Concepts Course University of Arizona 2 October 2014 Douglas Thain and Nicholas Hazekamp University of Notre Dame. Quick Recap. Makeflow = Make + Workflow. Provides portability across batch systems.

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Tutorial 12

Tutorial 12. Genome browser. Genome browser. Free, open source, online browser for genomes. Contains ~100 genomes, from nematodes to human. Many tools that can be used to analyze genomic data. Genome browser. http://genome.ucsc.edu/. How to find a gene of interest?. genome.

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Accessing and visualizing genomics data

Accessing and visualizing genomics data. Jim Noonan GENE 760. A working definition of genomics. The global study of how biological information is encoded in genome sequence Genes R egulatory sequences Genetic variation.

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Outline

Outline. Course outline Course website Bioinformatics facility account Lecture/discussion: Introduction to sequencing technologies. Intro: sequencing and the data deluge. Changes in instrument capacity over the past decade, and the timing of major sequencing projects.

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Genomes

Genomes. Daniel Lawson VectorBase @ EBI. Bioinformatic Tools for Comparative Genomics of Vectors. Tuesday 10:30 - 13:00 Genome sequencing 14:00 - 16:00 Genome annotation 16:30 - 18:00 Practical Wednesday 9:30 - 10:00 Review genome annotation 10:30 - 13:00 Comparative genomics I

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Whole-genome motif discovery

Whole-genome motif discovery. 7. 9. Challenges in Computational Biology. 4. Genome Assembly. Gene Finding. Regulatory motif discovery. DNA. Sequence alignment. Comparative Genomics. T C ATG C TAT T CG TGATA A TGA G GATAT T T AT C ATAT T T ATGAT T T. Database lookup.

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GigAssembler

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Phusion2 and The Genome Assembly of Tasmanian Devil

Phusion2 and The Genome Assembly of Tasmanian Devil. Zemin Ning The Wellcome Trust Sanger Institute. Outline of the Talk:. Challenges in genome assemblies from pure Illumina reads The Phusion2 pipeline The Tasmanian devil genome project The Devil genome assembly

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Computational Genomics BIOL 8803 A Spring 2011 King Jordan & Andy Conley

Computational Genomics BIOL 8803 A Spring 2011 King Jordan & Andy Conley Office hours by appointment: king.jordan@biology.gatech.edu 404-385-2224 Cherry Emerson 215 aconley@gatech.edu 404-385-1264 Cherry Emerson 217. Genomics & Computation.

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Large Plant Genome Assemblies using Phusion2

Large Plant Genome Assemblies using Phusion2. Zemin Ning The Wellcome Trust Sanger Institute. NGS Data. Assembly. Phusion2 Assembly Pipeline. Scaffolding Spinner. Mate Pair Reads 2k-40k. Pair End Reads 170-800bp. Consensus Bases Smalt & Gap5. Filtering Unikalow. Fermi.

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SWAP-Assembler: Scalable and Efficient Genome Assembly towards Thousands of Cores

SWAP-Assembler: Scalable and Efficient Genome Assembly towards Thousands of Cores. Jintao Meng, PH.D candidate Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Science, Shenzhen, China Recomb-seq 2014, Pittsburgh, 2014.3.31. Outline. Background

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Computational Genomics BIOL 7210 A Spring 2013 King Jordan & Andy Conley

Computational Genomics BIOL 7210 A Spring 2013 King Jordan & Andy Conley Office hours by appointment: king.jordan@biology.gatech.edu 404-385-2224 Cherry Emerson 215 aconley@gatech.edu 404-385-1264 Cherry Emerson 217. Genomics & Computation.

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De novo genome assembly

De novo genome assembly. Andrew Tritt September 13, 2012. Outline. Background Graphs Genome assembly Old ? Assembly in the Sanger days Overlap-layout-consensus New ? Assembly in the era of big data De Bruijn graphs Scaffolding ? utilizing paired-end data Hands On

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Cloud Architecture for Earthquake Science

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Lecture 14

Bioinformatics. Lecture 14. Genome sequencing projects Hierarchical and Shotgun approaches Genome assembly TIGR Assembler Ensembl. Genome size Mammalian genome ~ 3 megabase = 3x10 9 base pairs How many books are needed to print the entire mammalian genome?

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FHI Biotechnology Approaches

FHI Biotechnology Approaches. Clonal testing. New varieties. Marker-aided breeding. Transgenics. Genome sequencing. GE trees. Chestnut Genome Research Team. John E. Carlson, PI, Schatz Center, Penn State University. DNA Sequencing Stephan C. Schuster

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Short read alignment

Short read alignment. BNFO 601. Short read alignment. Input: Reads: short DNA sequences (upto a few hundred base pairs (bp)) produced by a sequencing machine Reads are fragments of a longer DNA sequence present in the sample given as input to the machine Usually in the millions

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Pacbio

Single Molecular Real-Time (SMRT) sequencing employs a specialized flow cell with many thousands of individual picolitre wells with transparent bottoms u2014 zero-mode waveguides (ZMW). The polymerase is fixed to the bottom of the well and allows the DNA strand to progress through the ZMW. As a result, the system can focus on a single molecular. https://www.cd-genomics.com/PacBio-SMRT-Sequencing.html

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