| Time | Description |
|---|---|
| 10:15-11:00 | Jenni Hultman: Introduction (including general structure of the course and group work) |
| 11.00-11.15 | Antti Karkman Setting up Visual Studio Code |
| 11.15-11:30 | Antti Karkman: Setting up the course folder |
| 11:30-12:00 | Antti Karkman: Nanopore trimming & QC - hands-on |
| 12:00-13:00 | Lunch 🍽️ |
| 13:00-14:00 | Jenni Hultman: Assembly hands-on |
| 14.00-14.30 | MBDP ☕ & 🍎 break |
| 14:00-17:45 | Jenni Hultman: Illumina trimming and QC |
PUHTI SERVICE BREAK (8-12)
| Time | Description |
|---|---|
| 10:15-11:00 | Antti Karkman: Polishing the assembly |
| 11:00-12:30 | Jenni Hultman: Assembly QC |
| 12:30-13:30 | Lunch 🍽️ |
| 14:00-17:00 | Video lecture: Reconstructing genomes from metagenomes - key concepts |
| 14:00-17:00 | Optional: Lars Paulin retirement seminar 🎂: From single nucleotides to large genomes using wide variety state-of-the-art sequencing technologies (Viikki, Bio2, 2041, pre-registeration needed) |
| Time | Description |
|---|---|
| 10:15-10:45 | Antti Karkman: Genome-Resolved Metagenomics |
| 10:45-12:00 | ALL: Preparing files for Anvio - hands-on |
| 12:00-13:00 | Lunch 🍽️ |
| 13:00-14:00 | ALL: Anvio cont' |
| 14.00-14.30 | MBDP ☕ & 🍎 break |
| 14:30-17:45 | Tatiana Demina : Viromics hands-on |
| 18:00-21:00 | Course dinner |
| Time | Description |
|---|---|
| 10:15-11:00 | Tatiana Demina Introduction to viromics |
| 11:00-12:00 | Jenni Hultman : Anvio hands-on cont' |
| 12:00-13:00 | Lunch 🍽️ |
| 13:00-14:00 | ALL: Anvio cont' |
| 14.00-14.30 | MBDP ☕ & 🍎 break |
| 14:30-16:30 | Jenni Hultman: Annotation with Bakta |
| 16:30-17:45 | Jenni Hultman: Metaphlan |
| Time | Description |
|---|---|
| 10:15-12:00 | Tatiana Demina : Viromics hands-on |
| 12:00-13:00 | Lunch 🍽️ |
| 13:00-14:00 | Antti Karkman : Metaphlan visualization |
| 14.00-14.30 | MBDP ☕ & 🍎 break |
| 14.30-15.00 | Antti Karkman : Metaphlan visualization |
| 15:00-17:45 | Q&A and Feedback |