; Technologies, applications and data analysis Course 2542 Dr. Martie C.M. Verschuren Research group Analysis techniques in Life Science, Breda Prof. dr. Johan T. den Dunnen Leiden Genome Technology Center, Leiden 2-4 April 2013 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 Breda
Code 2542 Tuesday April 2, 2013 Next generation sequencing technologies 08.45 Arrival and registration (Dr. Martie Verschuren, ) 09.00 General introduction to the course [2] (Dr. Martie Verschuren, ) 09.30 Overview NGS: General terminology and NGS sample preparation [3] (Dr. Henk Buermans, LUMC, Leiden) 10.10 Lecture: Roche / 454 technology and Ion Torrent platforms [4] (Ing. Marja Jakobs, AMC Amsterdam) 10.50 Coffee/Tea 11.05 Lecture: Illumina / Solexa and ABI / SOLID technology platform [5] (Dr. Ies Nijman, Hubrecht laboratory, Utrecht) 11.50 Lecture: Single molecule sequencing (Helicos biosciences, Pacific Biosciences and Oxford Nanopore platforms [6] (Ing. Yavuz Ariyurek, LUMC, Leiden) 12.40 Lunch Next generation sequencing applications 13.30 Lecture: Think before you start [7] (Dr. Judith Boer, Human Genetics, LUMC Leiden and Laboratory for Pediatric Oncology, Erasmus MC) 14.15 Lecture: RNA expression profiling [8] (Eleonora de Klerk of Peter Bram t Hoen, LUMC, Leiden) 15.00 Lecture: mirna profiling [9] (Dr. Henk Buermans, LUMC, Leiden) 15.45 Coffee/Thee 16.00 Computer practical, parallel sessions with Genome browser views on: RNA expression profiling and mirna profiling 18.00 End of the course day one. 18.30 Welcome Diner 20.30 The end of day one.
Code 2542 Wednesday April 3, 2013 Next generation sequencing applications 09.00 Welcome coffee and introduction of day 2 09.30 Lecture: Re-sequencing and detection of variants [10] (Dr. Victor Guryev, European Research Institute for the Biology of Ageing (ERIBA) 10.15 Lecture: ChIP-seq [11] (Dr.Wilfred van IJcken, Erasmus MC, Rotterdam) 11.00 Coffee/Thee 11.15 Lecture: DNA methylation sequencing [12] (Prof. Dr. Frank Johannes, Groningen Bioinformatics Centre, Groningen) 11.45 Computer practical, parallel sessions with Genome browser views on: Re-sequencing and detection of variants, Chip-seq and DNA methylation sequencing 13.30 Lunch 14.15 Lecture: De novo sequencing : a tool to discover novel pathways in microorganisms [13] (Huub Op den Camp, IWWR, Radboud University Nijmegen) Next generation sequencing data analysis 15.00 Lecture: Introduction to Nextgene data analysis [14] (Robert Akkers, Bioke) 15.30 Coffee/Thee 15.45 Computer practical: Windows practical: Nextgene data analysis (Robert Akkers, Bioke) 17.30 The end of day two.
Code 2542 Thursday April 4, 2013 Next generation sequencing data analysis 09.00 Welcome coffee and introduction day 3 09.30 Lecture: Metagenomics [15] (Dr. Sacha van Hijum, Nijmegen) 10.15 lecture: Introduction to CLCbio data analysis [16] (Patrick Dekker, CLCbio) 10.45 Coffee/Thee 11.00 Computer practical: Windows practical: CLCbio Workbench (Patrick Dekker, CLCbio) 13.00 Lunch 14.00 Lecture: Targeted sequencing [17] (Dr. Gijs Santen, LUMC, Leiden) 14.45 Other applications and future developments [18] (Prof.dr. Johan den Dunnen, LGTC, Leiden) 15.30 General discussion (Prof.dr. Johan den Dunnen, LGTC, Leiden) 16.30 Evaluation and official closing of the course 17.00 End of the course reserves the right to modify course materials or substitute speakers without notice.
; Data analysis Pipelines Course 2542b Dr. Martie C.M. Verschuren Research group Analysis techniques in Life Science, Breda Prof. dr. Johan T. den Dunnen Leiden Genome Technology Center, Human and clinical Genetics, LUMC, Leiden April 5, 2013 Research Group Analysis Techniques in Life Science P.O. Box 90116 4800 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 Breda
Code 2542b Friday April 5, 2013 EXTRA DAY Data analysis pipelines 09.00 General Introduction [3] 09.20 Lecture: Introduction to Linux [4] 09:40 Lecture: Command line and NGS tools [5] (Ing. Michiel van Galen, LGTC, Leiden) 10.10 Coffee/Thee 10:40 Lecture: Connecting to other machines [6] 11.10 Computer practical 1, General tools used in NGS: Command line practice. Splitting on bar codes. Alignment and SNP calling. (Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden) 12.00 Lunch 13.00 Lecture: NGS Pipelines [7] (Ing. Michiel van Galen, LGTC, Leiden) 13.30 Lecture: Galaxy and GAPSS [8] 14.00 Break 14.30 Computer practical 2, pipelines for complete analysis: Variant calling Expression analysis (CAGE). (Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden) 15.30 Questions and Discussion 16.00 End of the course reserves the right to modify course materials or substitute speakers without notice.