Next Generation Sequencing; Technologies, applications and data analysis

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1 ; Technologies, applications and data analysis Course 2542 Dr. Martie C.M. Verschuren Avans Hogeschool Research group Analysis techniques in Life Science, Breda Prof. dr. Johan T. den Dunnen Leiden Genome Technology Center, Leiden April 2015 Avans Hogeschool Research Group Analysis Techniques in Life Science P.O. Box RA Breda The Netherlands All rights reserved. No part of this publication may be reproduced or transmitted, in any form or by any means, without permission from Avans Hogeschool Breda

2 Code 2542 Tuesday April 14, 2015 Next generation sequencing technologies Arrival and registration (Dr. Martie Verschuren, Avans Hogeschool) General course introduction and NGS overview [2] (Dr. Martie Verschuren, Avans Hogeschool) NGS terminology & NGS sample preparation [3] (Dr. Henk Buermans, LUMC, Leiden) Lecture: Illumina / Solexa technology platform [4] (Dr. Ies Nijman, Hubrecht laboratory, Utrecht) Coffee/Tea Lecture: Ion Torrent platform [5] (Dr. Marcel Nelen, Radboud UMC, Nijmegen) Lecture: Single molecule sequencing [6] (Ing. Yavuz Ariyurek, LUMC, Leiden) Lunch Next generation sequencing Data analysis Introduction to NGS data analysis [7] Lecture: Operating systems basics [8] Lecture: Installing and updating software [9] Lecture: Getting started [10] break Lecture: Connecting to other machines [11]

3 16.00 Computer practical, covers the following: Connecting to a remote machine Using the command line Downloading and installing tools Running a simple analysis End of the course day one Welcome Diner End of day 1

4 Code 2542 Wednesday April 15, 2015 Next generation sequencing applications Welcome coffee and introduction of day Lecture: Think before you start [12] (Dr. Judith Boer, Human Genetics, LUMC Leiden and Laboratory for Pediatric Oncology, Erasmus MC) Lecture: NGS-based mrna profiling: from Tag-based approaches to Fulllength sequencing to investigate transcription, RNA processing and translation [13] (Eleonora de Klerk, LUMC, Leiden) Coffee/Thee Lecture: Re-sequencing and detection of variants [14] (Dr. Victor Guryev, European Research Institute for the Biology of Ageing (ERIBA) Lecture: NGS in DNA diagnostics [15] (Dr. Jasper Saris Erasmus MC, Rotterdam) Lunch Computer practical, parallel sessions with Genome browser views on: RNA expression analysis, Re-sequencing and detection of variants, DNA diagnostics Lecture: De novo sequencing: a tool to discover novel pathways in microorganisms [16] (Dr. Huub Op den Camp, IWWR, Radboud University Nijmegen) End of the course day two

5 Code 2542 Thursday April 16, 2015 Next generation sequencing applications Welcome coffee and introduction day Lecture: Metagenomics [17] (Dr. Sacha van Hijum, Nijmegen) Lecture: Comparative metagenomics using cross-assembly [18] (Dr. Bas Dutilh, Radboud UMC, Nijmegen) Coffee/Thee Lecture: DNA methylation sequencing [19] (Dr. Arjen Brinkman, NCMLS, Radboud University Nijmegen) Lecture: ChIP-seq [20] (Dr.Wilfred van IJcken, Erasmus MC, Rotterdam) Lunch Computer practical, parallel sessions with Genome browser views on:, Chip-seq, metagenomics, and DNA methylation sequencing Lecture: NGS applications in forensics [21] (Prof. Dr. Peter de Knijf, LUMC, Leiden) Lecture: NGS single cell analysis [22] (Dr. Thierry Voet, Leuven) End of day 3

6 Code 2542b Friday April 17, 2015 Next generation sequencing data analysis Welcome coffee and introduction day Lecture: Introduction to Nextgene data analysis [23] (Fons Elstrodt, Bioke) lecture: Introduction to CLCbio data analysis [24] (Niels Nielsen and Patrick Dekker, CLCbio/Qiagen) Coffee/Thee Computer practical: Windows practical: Nextgene data analysis (Fons Elstrodt, Bioke) or Computer practical: Windows practical: CLCbio Workbench (Niels Nielsen and Patrick Dekker, CLCbio/Qiagen) Lunch Data analysis pipelines Lecture: Combining tools into a pipeline [25] Computer practical, covers the following: Making a static shell script Variables Command line arguments Making a dynamic pipeline Break NGS: other applications and future developments [26] (Dr. Bart Janssen, ServiceXS, Leiden) General discussion (Dr. Bart Janssen, ServiceXS, Leiden)

7 17.15 Evaluation and official closing of the course End of the course Avans Hogeschool reserves the right to modify course materials or substitute speakers without notice.

Next Generation Sequencing; Technologies, applications and data analysis

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