Introduction to Next Generation Sequencing; technologies, applications and data analysis

DNA sequencing technologies are currently developing at an incredible speed and new applications are presented monthly, incl. DNA/RNA profiling, ChIP-seq, re-sequencing, de novo genome sequencing and metagenomics. The aim of this course is to introduce next generation sequencing technologies, highlight different applications of these new technologies, and show ways to analyse data.



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Participants:
This course has been developed for technicians and PhD students who are interested in, planning, or already working with next-generation sequencing. We welcome researchers from both the genomics and bioinformatics fields. Currently available technologies, applications, as well as hardware and software solutions will be presented and discussed.


Course structure:
We offer a three-day short-course consisting of a series of lectures on the technologies and applications of next generation sequencing and "hands-on" data analysis practicals. Furthermore we offer an additional course day for those partcipants who would like to get more skills in Linux based GAPSS data analysis pipelines. All participants will receive a practical manual containing all used protocols.


Topics included in the course:

3-day Course 2542
Next generation sequencing technologies and applications

preliminary course program:

Tuesday April 02, 2013

Lectures:
NGS: General terminology
Roche / 454 technology platform
ABI / SOLID technology platform
Illumina / Solexa technology platform
ChIP-seq
RNA expression profiling
miRNA profiling

Computer practicals:
Genome browser views: ChIP-seq, RNA expression profiling, and miRNA profiling


Wednesday April 03, 2013

Lectures:
Re-sequencing and SNP discovery
Hyb capture (array and in solution)
Paired end mapping
Targeted resequencing of oncogenes for mutation and copy number variation analysis sequencing
Introduction to Nextgene data analysis

Computer Practicals:
Genome browser views Re-sequencing, Hyb capture, and Paired end mapping
Windows practical: Nextgene data analysis


Thursday April 04, 2013

Lectures:
Metagenomics
Introduction to CLCbio data analysis
De novo sequencing: a tool to discover novel pathways in microorganisms
Future developments and single molecule sequencing

Computer practical:
Windows practical: CLCbio Workbench

EXTRA DAY Course 2542b
Data analysis pipelines
Preliminary course program:

Friday April 05, 2013

Lectures:
Intoduction to Linux
Alignment and assembly
Publicly available software
Introduction to pipelines and GAPSS

Computer practicals:
Linux practical, the basics
Alignment and assembly
GAPSS and UCSC viewing

Course leaders:
Dr. M.C.M. Verschuren, Avans Hogeschool, Research group Analysis Techniques in Life Science, Breda, NL
Course co-ordinator:
Dr. J.T. den Dunnen, Leiden Genome Technology Center, Human Genetics, LUMC, Leiden.

For more information and course fee, please visit our website.

2 Apr - 5 Apr 2013
Breda
Netherlands
meeting website