Next Generation Sequencing; Technologies, applications and data analysis

Transcription

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, Human and clinical Genetics, LUMC, Leiden March 2012 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 March 27, 2012 Next generation sequencing technologies Arrival, registration, coffee, and general introduction [2] (Dr. Martie Verschuren, ) Overview NGS: General terminology [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 technology platform [5] (Ing. Yavuz Ariyurek, LUMC, Leiden) Lecture: ABI / SOLID technology platform [6] (Dr. Ies Nijman, Hubrecht laboratory, Utrecht) Lunch Next generation sequencing applications Lecture: ChIP-seq [7] (Dr.Wilfred van IJcken, Erasmus MC, Rotterdam) Lecture: RNA expression profiling [8] (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: ChIP-seq, RNApressio0n profiling and mirna profiling End of the course day one.

3 Code 2542 Wednesday March 28, 2012 Next generation sequencing applications Welcome coffee and introduction of day Lecture: Re-sequencing and SNP discovery [10] (Dr. Hendrik-Jan Megens, WUR, Wageningen) Lecture: Paired end mapping [11] (Dr. Victor Guryev, Hubrecht laboratory, Utrecht) Coffee/Thee Lecture: targeted Sequencing[12] (Dr. Marjolein Kriek, LUMC, Leiden) Computer practical, parallel sessions with Genome browser views on: Re-sequencing, Hyb capture, and Paired end mapping Lunch Lecture: De novo sequencing : a tool to discover novel pathways in microorganisms [17] (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 March 29, 2012 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 resequencing of oncogenes for mutation and copy number variation analysis [13] (Dr. Peter Verhasselt, Johnson and Johnson, Belgium) Future developments and single molecule sequencing (Helicos) [18] (Prof.dr. Johan den Dunnen, LUMC, Leiden) General discussion (Prof.dr. Johan den Dunnen, LUMC, 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 March 30, 2012 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 March 30, 2012 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.