A hands-on introduction to Bioinformatics for Nanopore data from Influenza in the context of the IGS project. The workshop is held from March 8 to March 15, 2024 in Windhoek, Namibia.
- Torsten Houwaart, Franziska Kistner, Simon Tausch
All events are held at the Hilton Windhoek, conference room Haddis Junior 1.
| Time | Topic |
|---|---|
| 9:00-9:05 | Welcome |
| 9:05-11:00 | Navigate and manage the Linnux file system |
| 11:00-11:15 | Coffee break |
| 11:15-12:30 | View and modify files on the command line |
| 12:30-13:30 | Lunch |
| 13:30-13:45 | Wrap-up & questions |
| Time | Topic |
|---|---|
| 9:00-10:00 | Welcome & introduction |
| 10:00-11:00 | Introduction to next-generation sequencing & data analysis |
| 11:00-11:15 | Coffee break |
| 11:15-12:30 | Recap preparatory day |
| 12:30-13:30 | Lunch |
| 13:30-16:00 | View & modify files + intermediate commands |
| 15:00-15:15 | Coffee break |
| 16:00-16:16 | Wrap-up, questions & evaluation |
| Time | Topic |
|---|---|
| 9:00-9:30 | Recap Monday |
| 9:30-11:00 | Software installation via Conda (Input and Hands-On |
| 11:00-11:15 | Coffee break |
| 11:15-12:30 | Intermediate Command Line Commands |
| 12:30-13:30 | Lunch |
| 13:30-16:00 | Advanced Command Line (for-loops, basic scripts) |
| 15:00-15:15 | Coffee break |
| 15:15-16:00 | Nanopore data quality control |
| Time | Topic |
|---|---|
| 9:00-9:30 | Recap Tuesday |
| 9:30-11:00 | Advanced Command Line (for-loops, basic scripts, fastp) |
| 11:00-11:15 | Coffee break |
| 11:15-12:30 | Metagenomics with kraken2 (Input and Hands-On) |
| 12:30-13:30 | Lunch |
| 13:30-15:00 | Mapping (Input and Hands-On) |
| 15:00-15:15 | Coffee break |
| 15:15-16:00 | Variant Calling (Input and Hands-On) |
| Time | Topic |
|---|---|
| 9:00-9:30 | Recap Wednesday |
| 9:30-11:00 | Consensus, Typing (Input and Hands-On) |
| 11:00-11:15 | Coffee break |
| 11:15-12:30 | Repetition (Challenge) |
| 12:30-13:30 | Lunch |
| 13:30-15:00 | Workflows (Input and Hands-On) |
| 15:00-15:15 | Coffee break |
| 15:15-16:00 | Repetition (Challenge) |
| Time | Topic |
|---|---|
| 9:00-9:30 | Recap Thursday |
| 9:30-11:00 | Bring your own data |
| 11:00-11:15 | Coffee break |
| 11:15-12:30 | Bring your own data |
| 12:30-13:30 | Lunch |
Evaluation sheet: https://docs.google.com/forms/d/e/1FAIpQLScv2Zprkgp6DYNm7s99ud5QHeUnJkuA1q6f__Aa1EtmFzuWIw/viewform?usp=sf_link