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 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 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

2 Code 2542 Tuesday April 2, 2013 Next generation sequencing technologies Arrival and registration (Dr. Martie Verschuren, ) General introduction to the course [2] (Dr. Martie Verschuren, ) Overview NGS: General terminology and NGS sample preparation [3] (Dr. Henk Buermans, LUMC, Leiden) Lecture: Roche / 454 technology and Ion Torrent platforms [4] (Ing. Marja Jakobs, AMC Amsterdam) Coffee/Tea Lecture: Illumina / Solexa and ABI / SOLID technology platform [5] (Dr. Ies Nijman, Hubrecht laboratory, Utrecht) Lecture: Single molecule sequencing (Helicos biosciences, Pacific Biosciences and Oxford Nanopore platforms [6] (Ing. Yavuz Ariyurek, LUMC, Leiden) Lunch Next generation sequencing applications Lecture: Think before you start [7] (Dr. Judith Boer, Human Genetics, LUMC Leiden and Laboratory for Pediatric Oncology, Erasmus MC) Lecture: RNA expression profiling [8] (Eleonora de Klerk of Peter Bram t Hoen, LUMC, Leiden) Lecture: mirna profiling [9] (Dr. Henk Buermans, LUMC, Leiden) Coffee/Thee Computer practical, parallel sessions with Genome browser views on: RNA expression profiling and mirna profiling End of the course day one Welcome Diner The end of day one.

3 Code 2542 Wednesday April 3, 2013 Next generation sequencing applications Welcome coffee and introduction of day Lecture: Re-sequencing and detection of variants [10] (Dr. Victor Guryev, European Research Institute for the Biology of Ageing (ERIBA) Lecture: ChIP-seq [11] (Dr.Wilfred van IJcken, Erasmus MC, Rotterdam) Coffee/Thee Lecture: DNA methylation sequencing [12] (Prof. Dr. Frank Johannes, Groningen Bioinformatics Centre, Groningen) Computer practical, parallel sessions with Genome browser views on: Re-sequencing and detection of variants, Chip-seq and DNA methylation sequencing Lunch 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 Lecture: Introduction to Nextgene data analysis [14] (Robert Akkers, Bioke) Coffee/Thee Computer practical: Windows practical: Nextgene data analysis (Robert Akkers, Bioke) The end of day two.

4 Code 2542 Thursday April 4, 2013 Next generation sequencing data analysis Welcome coffee and introduction day Lecture: Metagenomics [15] (Dr. Sacha van Hijum, Nijmegen) lecture: Introduction to CLCbio data analysis [16] (Patrick Dekker, CLCbio) Coffee/Thee Computer practical: Windows practical: CLCbio Workbench (Patrick Dekker, CLCbio) Lunch Lecture: Targeted sequencing [17] (Dr. Gijs Santen, LUMC, Leiden) Other applications and future developments [18] (Prof.dr. Johan den Dunnen, LGTC, Leiden) General discussion (Prof.dr. Johan den Dunnen, LGTC, Leiden) Evaluation and official closing of the course End of the course reserves the right to modify course materials or substitute speakers without notice.

5 ; 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 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

6 Code 2542b Friday April 5, 2013 EXTRA DAY Data analysis pipelines General Introduction [3] Lecture: Introduction to Linux [4] 09:40 Lecture: Command line and NGS tools [5] (Ing. Michiel van Galen, LGTC, Leiden) Coffee/Thee 10:40 Lecture: Connecting to other machines [6] 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) Lunch Lecture: NGS Pipelines [7] (Ing. Michiel van Galen, LGTC, Leiden) Lecture: Galaxy and GAPSS [8] Break Computer practical 2, pipelines for complete analysis: Variant calling Expression analysis (CAGE). (Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden) Questions and Discussion End of the course reserves the right to modify course materials or substitute speakers without notice.

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