; 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 14-17 April 2015 Avans Hogeschool Research Group Analysis Techniques in Life Science P.O. Box 90116 4800 RA Breda The Netherlands www.alsavans.nl 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
Code 2542 Tuesday April 14, 2015 Next generation sequencing technologies 08.45 Arrival and registration (Dr. Martie Verschuren, Avans Hogeschool) 09.00 General course introduction and NGS overview [2] (Dr. Martie Verschuren, Avans Hogeschool) 09.45 NGS terminology & NGS sample preparation [3] (Dr. Henk Buermans, LUMC, Leiden) 10.25 Lecture: Illumina / Solexa technology platform [4] (Dr. Ies Nijman, Hubrecht laboratory, Utrecht) 10.55 Coffee/Tea 11.10 Lecture: Ion Torrent platform [5] (Dr. Marcel Nelen, Radboud UMC, Nijmegen) 11.50 Lecture: Single molecule sequencing [6] (Ing. Yavuz Ariyurek, LUMC, Leiden) 12.30 Lunch Next generation sequencing Data analysis 13.30 Introduction to NGS data analysis [7] 13.45 Lecture: Operating systems basics [8] 14.00 Lecture: Installing and updating software [9] 14.30 Lecture: Getting started [10] 15.00 break 15.30 Lecture: Connecting to other machines [11]
16.00 Computer practical, covers the following: Connecting to a remote machine Using the command line Downloading and installing tools Running a simple analysis 17.30 End of the course day one 18.30 Welcome Diner 20.30 End of day 1
Code 2542 Wednesday April 15, 2015 Next generation sequencing applications 09.00 Welcome coffee and introduction of day 2 09.30 Lecture: Think before you start [12] (Dr. Judith Boer, Human Genetics, LUMC Leiden and Laboratory for Pediatric Oncology, Erasmus MC) 10.15 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) 11.00 Coffee/Thee 11.15 Lecture: Re-sequencing and detection of variants [14] (Dr. Victor Guryev, European Research Institute for the Biology of Ageing (ERIBA) 12.00 Lecture: NGS in DNA diagnostics [15] (Dr. Jasper Saris Erasmus MC, Rotterdam) 12.45 Lunch 13.45 Computer practical, parallel sessions with Genome browser views on: RNA expression analysis, Re-sequencing and detection of variants, DNA diagnostics 16.45 Lecture: De novo sequencing: a tool to discover novel pathways in microorganisms [16] (Dr. Huub Op den Camp, IWWR, Radboud University Nijmegen) 17.30 End of the course day two
Code 2542 Thursday April 16, 2015 Next generation sequencing applications 09.00 Welcome coffee and introduction day 3 09.30 Lecture: Metagenomics [17] (Dr. Sacha van Hijum, Nijmegen) 10.15 Lecture: Comparative metagenomics using cross-assembly [18] (Dr. Bas Dutilh, Radboud UMC, Nijmegen) 11.00 Coffee/Thee 11.15 Lecture: DNA methylation sequencing [19] (Dr. Arjen Brinkman, NCMLS, Radboud University Nijmegen) 11.45 Lecture: ChIP-seq [20] (Dr.Wilfred van IJcken, Erasmus MC, Rotterdam) 12.30 Lunch 13.30 Computer practical, parallel sessions with Genome browser views on:, Chip-seq, metagenomics, and DNA methylation sequencing 16.00 Lecture: NGS applications in forensics [21] (Prof. Dr. Peter de Knijf, LUMC, Leiden) 16.45 Lecture: NGS single cell analysis [22] (Dr. Thierry Voet, Leuven) 17.30 End of day 3
Code 2542b Friday April 17, 2015 Next generation sequencing data analysis 09.00 Welcome coffee and introduction day 4 09.15 Lecture: Introduction to Nextgene data analysis [23] (Fons Elstrodt, Bioke) 09.45 lecture: Introduction to CLCbio data analysis [24] (Niels Nielsen and Patrick Dekker, CLCbio/Qiagen) 10.15 Coffee/Thee 10.30 Computer practical: Windows practical: Nextgene data analysis (Fons Elstrodt, Bioke) or Computer practical: Windows practical: CLCbio Workbench (Niels Nielsen and Patrick Dekker, CLCbio/Qiagen) 12.30 Lunch Data analysis pipelines 13.15 Lecture: Combining tools into a pipeline [25] 13.45 Computer practical, covers the following: Making a static shell script Variables Command line arguments Making a dynamic pipeline 15.15 Break 15.30 NGS: other applications and future developments [26] (Dr. Bart Janssen, ServiceXS, Leiden) 16.30 General discussion (Dr. Bart Janssen, ServiceXS, Leiden)
17.15 Evaluation and official closing of the course 17.30 End of the course Avans Hogeschool reserves the right to modify course materials or substitute speakers without notice.