Workshop Nanopore Bioinformatics

A practical introduction to ONT, Linux, and bacteria long-read genome reconstruction for NGS Summerschool.

Schedule links for the workshop

• XXXX-XX-XX - Someday: First day: Learn the basic (from raw reads to assembly)
• XXXX-XX-XX - Someday: Final day: Miscellaneous

Instructors

• ............

Summary Cheat Sheet

Cheat Sheet

Schedule

All events are held at ..............

Someday, XXXX-XX-XX

Time	First day: Learn the basic (from raw reads to assembly)
09:00-09:15	Welcome & introduction
09:15-09:30	Linux crash course
09:30-10:00	Hands-on: Setup machines
10:00-10:15	Coffee break
10:15-11:00	Hands-on: Data management & ONT QC
11:00-12:00	Hands-on: Long read assembly
12:00-13:00	Lunch break
13:00-14:00	Hands-on: Polishing with long reads
14:00-14:30	Bonus: Polishing with short reads
14:30-15:00	Bonus: Assembly analysis

Someday, XXXX-XX-XX

Time	Final day & Miscellaneous
09:00-09:30	Setup & Debriefing Day 1
09:00-11:45	Working on own sequencing data
11:45-12:00	Wrap up

Acknowledgement

This course material is partly based on the following resources and on contributions from great people:

• Sebastian "Raverjay" Krautwurst, FSU Jena, some Linux and ONT content
• Stephan Fuchs, RKI MF1, some Linux and Assembly content
• Matt Huska, RKI MF1, automatic test script for all md code blocks using codedown and general help
• Workshop structure inspired by https://github.com/cinemaparis/2023
• Some ONT intro slides from Josh Quick, original
• Nanopore long-read bioinformatics tutorial from timkahlke