4 April 2016
Time Topic (Health Teaching Labs 1)
8:30 Registration
9:00  Welcome address
9:10  Participant introductions
9:30 Introduction to NGS file formats and workflows (Talk)
10:10 Introduction to the web based Galaxy platform for NGS analysis (Talk)
10:25  Register for a Galaxy account (Practical)
10:30 am  Tea break (Student Cafeteria)
11:00 Uploading data into Galaxy, tools, histories and workflow sharing (Practical) (Galaxy basics workflow)
11:20 Preprocessing and QC of NGS data (Talk)
11:40 Examining FASTQ files in Galaxy, pre-processing and quality control of NGS data (Practical)
12:20 Alignment of reads, reference sequence, indel realignment (Talk)
12:40 Submit alignment jobs to Galaxy (Practical)
1:00  Lunch
2:00  Alignment of reads, post processing, obtaining statistics, visualising alignments (Practical)
3:00 Introduction_to_variant_calling (Talk)
3:20 Submit variant calling jobs to Galaxy (Practical)
3:30  Tea Break
4:00  VCF file format and tools for manipulation, visualization (Practical)
Practical material for day 1:
Complete Galaxy SNP calling workflow used in the practicals
Practical instructions
5:00  Workshop End
5 April 2016
9:00 Recap of previous days activities and Q and A session
9:30 Overview of variant prioritisation. Introduction to genome databases. (Talk)
(Practical) (EnsemblBiomart extra)
10:30  Tea Break (Student Cafeteria)
11:00  Exploring genome databases (Practical)
12:00  Lunch (IIDMM Cafeteria)
1:00 NGS variant analysis: Annotation and filtering (Talk)
2:30  Tea Break
3:00 NGS variant analysis: Exploring links to phenotype and biological function (Talk)
(Practical) (VCF used in Practical) (wANNOVAR annotation generated in Practicall) (VCF format specifications)
5:00  Workshop End
6 April 2016
9:00  Recap of previous days activities and Q and A session
9:30  Findable, accessible, interoperable and reusable (FAIR) Data in Life Sciences (Talk)
10:30  Tea break (Student Cafeteria)
11:00  Gene-­‐disease investigation in integrated datasets (Practical)
12:30  Lunch (IIDMM Cafeteria)
1:30  Introduction to pharmacogenomics (Talk)
1:45  Setting up a pharmacogenomics study: important considerations (Talk)
3:00  Tea break (Student Cafeteria)
3:30 Pharmacokinetics and pharmacogenetics of rosuvastatin (Talk)
4:00  Discussion of project ideas (Group discussion led by Prof. Collet Dandara)
5:00 Workshop End