| 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 | Genomics Mirko Rossi: Basic usage of cPouta cloud computing service at CSC |
| 09:45-10:45 | Genomics 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 | Genomics João Carriço: Making Use of NGS Data: From Reads to Trees and Annotations |
| 12:00-13:30 | Working with your data and lunch |
| 13:30-17:00 | Genomics Miguel Machado: From reads to assemblies: working with INNUca pipeline |
| Time | Description |
|---|---|
| 08:30-11:45 | Genomics Miguel Machado: In silico typing using ReMatCh and Abricate |
| 12:00-13:30 | Working with your data and lunch |
| 13:30-16:00 | Genomics Mickael Silva: Whole genome and core genome MLST analysis using chewBBACA suite (see also chewBBACA wiki) |
| 16:00-17:00 | Working with your data |
| Time | Description |
|---|---|
| 08:30-10:45 | Genomics Miguel Machado & Bruno Gonçalves: Annotation (PROKKA), pangenome anaylysis (ROARY) and GWAS (SCOARY) |
| 11:00-12:30 | Working with your data and lunch |
| 12:30-14:30 | Genomics Bruno Gonçalves: Integrating phylogenetic inference and metadata visualization for NGS data |
| 14:30-15:30 | Metagenomics Antti Karkman: Data download, QC (FASTQC) and trimming (CUTADAPT) |
| 15:30-17:00 | Metagenomics Jenni Hultman: Assembly (MEGAHIT) and installation of programs |
| Time | Description |
|---|---|
| 08:00-10:00 | Metagenomics Jenni Hultman: Assembly check and mapping with (BOWTIE2) |
| 10:00-12:00 | Metagenomics Antti Karkman: Read based analysis for 16S rRNA (Metaxa2) and ARG (ResFinder) |
| 12:00-14:00 | Working with your data and lunch |
| 14:00-17:00 | Metagenomics Antti Karkman and Jenni Hultman: Prepping files for Anvio |
| Time | Description |
|---|---|
| 09:00-10:00 | Metagenomics Tom Delmont: Introduction to Anvio NB. Room 2012 Biocenter 2 AND coffee and pulla |
| 10:30-12:00 | Metagenomics Tom Delmont: Metagenome visualization in Anvio (ANVIO) |
| 12:00-13:00 | Working with your data and lunch |
| 13:00-16:00 | Metagenomics Tom Delmont: Construction of MAGs with Anvio |
| 16:00-17:00 | Metagenomics Jenni Hultman: Wrapping up |