Course Date: April 02-5, 2013, Breda (NL) Last update: 16-01-2013
This course is organised in collaboration with Dr. J.T. den Dunnen, Leiden Genome Technology Center, Human Genetics, LUMC, Leiden
of the course:
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.
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.
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:
Next generation sequencing technologies and applications
preliminary course program:
Tuesday April 02, 2013
Overview NGS: General terminology and NGS sample preparation
Roche / 454 technology and Ion Torrent platforms
Illumina / Solexa and ABI / SOLID technology platform
Single molecule sequencing (Helicos biosciences, Pacific Biosciences and Oxford Nanopore platforms)
Think before you start
RNA expression profiling
Genome browser views: RNA expression profiling and miRNA profiling
Wednesday April 03, 2013
Re-sequencing and detection of variants
Whole Genome Bisulphite sequencing
De novo sequencing
Introduction to Nextgene data analysis
Genome browser views ChIP-seq, Re-sequencing and detection of variants, Genome Bisulphite sequencing
Windows practical: Nextgene data analysis
Thursday April 04, 2013
Introduction to CLCbio data analysis
Future developments and single molecule sequencing
Windows practical: CLCbio Workbench
EXTRA DAY Course 2542b
Data analysis pipelines
Preliminary course program:
Friday April 05, 2013
Intoduction to Linux
Alignment and assembly
Publicly available software
Introduction to pipelines and GAPSS
Linux practical, the basics
Alignment and assembly
GAPSS and UCSC viewing
Avans Hogeschool reserves the right to substitute speakers, and change the theoretical and practical program, in order to cover most current and future new sequening technologies applications.
Dr. M.C.M. Verschuren, Avans Hogeschool, Research group Analysis Techniques in Life Science, Breda, NL
Dr. J.T. den Dunnen, Leiden Genome Technology Center, Human Genetics, LUMC, Leiden.
All participants will receive a certificate of attendance
Code: 2542 (3-day course)
Registration fee: € 900,- The fee includes course materials, lunch and welcome diner. Handouts will be provided in the course map in black&white and all participants will receive digital handouts in full color.
Code: 2542b (1 day additional course)
Registration fee: € 300,- The fee includes course materials and lunch. Handouts will be provided in the course map in black&white and all participants will receive digital handouts in full color.
Location : Avans Hogeschool, Lovensdijkstraat 61, Breda, The Netherlands route description