NGS - Quality control, Alignment, Visualisation - February 2017
Section outline
-
NGS - Quality control, Alignment, Visualisation
09-10 February 2017
Bern, Hochschulstrasse 4 - Seminarraum Nr. 331/3. OG West, University of Bern
This page is addressed to registered participants. To access course description and application form, please click here.
This course will be taught by Walid Gharib, for any assistance, please contact training@sib.swiss.
-
Thursday 09 February
Introduction to technologies and applications, NCBI E-Utilities and sequencing data retrieval
9:15 - 10:30 - Introduction to technologies and applications (1)
- Roche 454 - Pyrosequencing
- llumina - sequencing by synthesis
10:30 - 11:00 - Coffee Break
11:30 - 12:15 - Introduction to technologies and applications (2)
- Pacific Biosciences - SMRT Sequencing
- Ion Torrent Sequencing - Semiconductor sequencing
12:15 - 13:30 - Lunch Break
13:30 - 13:45 - NCBI: E-utilities using Unix command line
13:45 - 15:00 - E-utilities usage - Practicals15:00 - 15:30 - Coffee break
15:30 - 15:45 - Sequencing archives, SRA, ENA and DDBJ
15h45 - 17:00 - Fetching sequencing data - Practicals (Combining E-utilities and SRA tools)Friday 10 February
File Formats, quality assessment, cutting/trimming/filtering and sequence alignement
9:00 - 10:00: File formats and Quality controls
9:45 - 10:30: Interpretation of a Fastqc report and acting upon for cutting/trimming reads10:30 - 11:00: Coffee break
11:00 - 12:15: Quality control - Practicals
- Trimming/filtering quality control - Practicals
12:15 - 13:30 - Lunch Break
13:30 - 15:30 - Alignment to a reference genome - Small intro and practicals
16:00 - 17:00 - Sorting, Indexing the alignment and quick visualization using IGV genome viewer -
Participants should install "The Integrative Genome Viewer (IGV)" on their respective machines.
Basic understanding of working with command line tools on Linux or Windows-based operating systems is required. If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals e-learning module.