Leipzig Summer School, Day 5 Viromics

Welcome to the 2024 Leipzig Summer School, Day 5 workshop.

Helmholtz Centre for Environmental Research

12 July 2024          9:45 AM - 5:00 PM CEST

Instructors: Noriko Cassman, Shahram Saghaei

Helpers: Shahram Saghaei, Martin Bole, Jonas Kasmanas


General Information

Who: The course is aimed at graduate students and other researchers with little to no bioinformatics experience. You don’t need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Helmholtz Centre for Environmental Research (Permoserstraße 15, 04318 Leipzig). Get directions with Google Maps.

When: 12 July 2024; 9:45 AM - 5:00 PM CEST Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.


Setup

To participate in a Practical part of this workshop, you will need access to software as described below.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The setup instructions for the workshop can be found at the workshop overview site.


Disclaimer

This workshop uses the workshop template of the Carpentries, but is not part of the official Carpentries curriculum. Part of this workshop has been modified from prior Viromics Workshops (https://mgxlab.github.io/Viromics-Workshop-MGX and https://github.com/MGXlab/Viromics2024) by the Virus Ecology Group of the Microverse (https://www.bio.uni-jena.de/en/2235/viral-ecology-and-omics).

Schedule

Setup Download files required for the lesson
09:45 1. Introduction & Setup
10:15 2. Lecture on Viruses and viromics
10:45 3. Break and Questions
11:15 4. Lecture on RDM and Virus Infrastructure
11:45 5. Lunch break
12:45 6. Project Explanation
13:15 7. Exploring viromics resources and files What are the data sources in viromics
13:45 8. Quality control and taxonomic profiling Quality control and taxonomic profiling of one virome
14:15 9. Virome Assembly and Bin Evaluation How to bin virus genomes from the assembly file
How to evaluate binning results
14:45 10. Virus identification using geNomad How to use geNomad?
15:15 11. Wrap Up
15:45 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.