| Time | Description |
|---|---|
| 09:00-09:30 | Jenni Hultman and Mirko Rossi: Introduction (including general structure of the course and group work) |
| 09:30-09:45 | Mirko Rossi: Basic usage of cPouta cloud computing service at CSC |
| 09:45-10:45 | Mirko Rossi: Prepare the Virtual Machine |
| 10:45-11:00 | break - Note: the coffee break is not included in the course |
| 11:00-11:45 | João Carriço: Making Use of NGS Data: From Reads to Trees and Annotations |
| 11:45-12:00 | Mirko Rossi: Working in group instruction, part 1 |
| 12:00-13:30 | Working with your data and lunch |
| 13:30-17:00 | Miguel Machado: From reads to assemblies: working with INNUca pipeline |
| Time | Description |
|---|---|
| 08:30-10:45 | Miguel Machado: From reads to assemblies: working with INNUca pipeline |
| 10:45-11:00 | break - Note: the coffee break is not included in the course |
| 11:00-12:00 | Mirko Rossi: Working in group instruction, part 1 |
| 12:00-13:00 | Working with your data and lunch |
| 13:00-15:20 | Miguel Machado & João Carriço: In silico typing using ReMatCh and Abricate |
| 15:20-15:30 | break - Note: the coffee break is not included in the course |
| 15:30-17:00 | Mirko Rossi & Miguel Machado: Annotation with Prokka and intro of Roary |
| Time | Description |
|---|---|
| 08:30-10:45 | Mickael Silva: Whole genome and core genome MLST analysis using chewBBACA suite (see also chewBBACA wiki) |
| 10:45-11:00 | break - Note: the coffee break is not included in the course |
| 11:00-11:30 | Mirko Rossi: Working in group instruction, part 2 |
| 11:30-12:30 | Working with your data and lunch |
| 12:30-14:30 | Bruno Gonçalves: Integrating phylogenetic inference and metadata visualization for NGS data |