Programme
Section outline
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Monday 7 September
Introduction to technologies and applications, NCBI E-Utilities and sequencing data retrieval
9:15 - 9:45 - UNIX reminder
9:45 - 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)Tuesday 8 September
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
12:15 - 13:30 - Lunch Break
13:30 - 15:30 - Trimming/filtering quality control - Practicals
16:00 - 17:00 - Alignment to a reference genome - Small intro and practicals
17:00 - 17:05 - Two words about the upcoming NGS modules