Next Generation Sequencing

Next Generation Sequencing;
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
1-4 April 2014
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
International Post-graduate Course
Next Generation Sequencing
Code 2542
Tuesday April 1, 2014
Next generation sequencing technologies
08.45
Arrival and registration
(Dr. Martie Verschuren, Avans Hogeschool)
09.00
General course introduction and NGS overview [B]
(Dr. Martie Verschuren, Avans Hogeschool)
09.45
NGS terminology & NGS sample preparation [C]
(Dr. Henk Buermans, LUMC, Leiden)
10.25
Lecture: Illumina / Solexa technology platform [E]
(Dr. Ies Nijman, Hubrecht laboratory, Utrecht)
10.55
Coffee/Tea
11.10
Lecture: Ion Torrent platform [D]
(André Wijfjes, ServiceXS B.V. Leiden)
11.50
Lecture: Single molecule sequencing [F]
(Ing. Yavuz Ariyurek, LUMC, Leiden)
12.30
Lunch
Next generation sequencing Data analysis
13.30
General Introduction to data analysis [3]
(Dr. Jeroen Laros, LGTC, Leiden)
13.50
Lecture: Introduction to Linux [4]
(Dr. Jeroen Laros, LGTC, Leiden)
14:10
Lecture: Command line and NGS tools [5]
(Ing. Michiel van Galen, LGTC, Leiden)
14.40
break
15:00
Lecture: Connecting to other machines [6]
(Dr. Jeroen Laros, LGTC, Leiden)
15.30
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)
17.30
End of the course day one
18.30
Welcome Diner
20.30
End of day 1
International Post-graduate Course
Next Generation Sequencing
Code 2542
Wednesday April 2, 2014
Next generation sequencing applications
09.00
Welcome coffee and introduction of day 2
09.30
Lecture: Think before you start [G]
(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 [H]
(Eleonora de Klerk, LUMC, Leiden)
11.00
Coffee/Thee
11.15
Lecture: miRNA profiling [IJ]
(Dr. Henk Buermans, LUMC, Leiden)
12.00
Lecture: NGS in DNA diagnostics [TU]
(Dr. Jasper Saris Erasmus MC, Rotterdam)
12.45
Lunch
13.45
Computer practical, parallel sessions with Genome browser views on:
RNA expression analysis, miRNA profiling, DNA diagnostics
16.45
Lecture: De novo sequencing: a tool to discover novel pathways in microorganisms [NO]
(Dr. Huub Op den Camp, IWWR, Radboud University Nijmegen)
17.30
End of the course day two
International Post-graduate Course
Next Generation Sequencing
Code 2542
Thursday April 3, 2014
Next generation sequencing applications
09.00
Welcome coffee and introduction day 3
09.30
Lecture: Metagenomics [R]
(Dr. Sacha van Hijum , Nijmegen)
10.15
Lecture: DNA methylation sequencing [M]
(Dr. Arjen Brinkman, NCMLS, Radboud University Nijmegen)
11.00
Coffee/Thee
11.15
Lecture: Re-sequencing and detection of variants [K]
(Dr. Victor Guryev, European Research Institute for the Biology of Ageing
(ERIBA)
11.45
Lecture: ChIP-seq [L]
(Dr.Wilfred van IJcken, Erasmus MC, Rotterdam)
12.30
Lunch
13.30
Computer practical, parallel sessions with Genome browser views on:
Re-sequencing and detection of variants, Chip-seq and DNA methylation
sequencing
16.00
Lecture: eDNA [R]
(Kevin Beentjes, Naturalis, Leiden)
16.45
Lecture: NGS single cell analysis
(Dr. Thierry Voet, Leuven)
17.30
End of day 3
International Post-graduate Course
Next Generation Sequencing
Code 2542b
Friday April 4, 2014
Next generation sequencing data analysis
09.00
Welcome coffee and introduction day 4
09.15
Lecture: Introduction to Nextgene data analysis [PQ]
(Fons Elstrodt, Bioke)
09.45
lecture: Introduction to CLCbio data analysis [S]
(Sarah Nema, CLCbio)
10.15
Coffee/Thee
10.30
Computer practical:
Windows practical: Nextgene data analysis
(Fons Elstrodt, Bioke)
or
Computer practical:
Windows practical: CLCbio Workbench
(Sarah Nema, CLCbio)
12.30
NGS: other applications and future developments [V]
(Prof.dr. Johan den Dunnen, LGTC, Leiden)
13.15
Lunch
Data analysis pipelines
14.00
Lecture: NGS Pipelines [7]
(Ing. Michiel van Galen, LGTC, Leiden)
14.30
Lecture: Galaxy and GAPSS [8]
(Dr. Jeroen Laros, LGTC, Leiden)
15.00
Break
15.30
Computer practical 2, pipelines for complete analysis:
 Variant calling
 Expression analysis (CAGE).
(Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden)
16.30
General discussion
(Prof.dr. Johan den Dunnen, LGTC, 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.

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