Day 1:

Introduction to the command line, the conda package manager and the bash scripting language. Downloading and annotating.

9:00 – 9:15   Introduction and course overview

9:15 – 10:00: Interactive lecture [Le1]: setting up the command line (prior Linux install is expected)

10:00 – 12:00: Interactivate Linux exercises – navigating, copying and loops

12:00 – 13:00: Lunch

13:00 – 14:00: Lecture [Le2]: Basic genome assembly and what we can download.

14:00 – 15:00: Genome download & overview – how & what software?

15:00 – 17:00: Genome annotation – new environments and our first loop

Day 2:

Finding the functional gene content and building a phylogeny

9:00 – 9:30:   Recap and follow up [Le3] – the hard parts of bioinformatics?

9:30 – 10:00: Lecture [Le4] – annotation of phages and BGCs

10:00 – 11:00: Prophage annotation – another loop, another package

11:00 – 12:00: BGC annotation – yet another loop and a different package

12:00 – 13:00: Lunch

13:00 – 14:00: Phylogeny, Trees and Genotypes [Le5]

14:00 – 16:00: Building a core genome phylogenetic tree and finding patterns

Day 3:

Trip to Bela krajina and presentations

Day 4:

Long-read metagenomics: filtering and assembling metagenomic data

9:00 – 9:30:   Lecture [Le6] – Nanopore sequencing

9:30 – 10:00: Lecture [Le7] – Nanopore metagenomics

10:00 – 10:30: Downloading data

11:00 – 12:00: Filtering and assembling metagenomes

12:00 – 13:00: Lunch

13:00 – 16:00: Free play with what you learned from the single genomes!

Day 5:

Introduction to R and Rstudio, installing R packages. The concepts of metataxonomics and the DADA2 pipeline

9:00 – 9:30     Company lecture

9:15 – 10:00:   Interactive lecture [Le8]: setting up Rstudio projects

10:00 – 11:00: R basics [Le9]: navigating, installing and plotting

11:00 – 12:00: Lecture [Le10]: Metataxonomics as a concept.

12:00 – 13:00: Lunch

13:00 – 15:00: Downloading and bioinformatic analysis of data

15:00 – 16:00: Wrapping up and goodbye!