Programme

12 June

Introduction to technologies and applications, NCBI E-Utilities and sequencing data retrieval  

9:15 - 10:30 - Introduction to technologies and applications (1)

• Ion Torrent Sequencing - Semiconductor sequencing
  
• llumina - sequencing by synthesis

10:30 - 11:00 - Coffee Break

11:30 - 12:15 - Introduction to technologies and applications (2)

• Pacific Biosciences - SMRT Sequencing
• Oxford Nanopores - MinIon, GridIon

12:15 - 13:30 - Lunch Break

13:30 - 13:45 - NCBI: E-utilities using Unix command line
13:45 - 15:00 - E-utilities usage - Practicals

15:00 - 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)

13 June

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 reads

10:30 - 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
15h30 - 17:00 -  Sorting, Indexing the alignment and quick visualization using IGV genome viewer

14 June

9:00 - 10:30: Visualisation using IGV lecture 
10:30 - 11:00: Coffee break

11:00 - 12:15:  Practicals using cancer variants dataset

12:15 - 13:30: Lunch Break

13:30 - 15:30: Practicals using RNAseq and CHIPseq datasets