Workshop Synopsis: Unveiling Viruses - Viral Metagenomics and Viral Genome Reconstruction
Information about the pre-workshop can be dowloaded here>>
Target Audience
PhD Students and Postdocs in metagenomics and adjescent fields.
Prerequisites
Basic understanding of command-line interface (CLI) usage.
Prior experience with bioinformatics concepts (desirable but optional).
Familiarity with Unix-based systems or willingness to use Windows Subsystem for Linux 2 (WSL2) for Docker setup.
Format
A separate 1h pre-workshop virtual session plus a 2h hands-on workshop in Stockholm
Datasets
Influenza & Mpox metagenomic data
Software
Docker (native Unix or WSL2 on Windows)
Hardware requirements
Windows:At least 12 cores, 32Gb RAM and 250Gb of HDD/SSD
Mac: At least 8 cores, 16Gb RAM and 250Gb of HDD/SSD
Linux: At least 12 cores, 16Gb RAM and 250Gb of HDD/SSD
Background
In the last decade, the field of viral metagenomics has emerged as a powerful tool for studying the genetic material of the virome directly from clinical samples. Viral metagenomics allows researchers to explore the diversity and dynamics of viral populations within complex biological samples, offering insights into viral ecology, evolution, and their role in disease.
As our understanding of viruses evolves, so does the need for advanced methodologies to unravel their complexities. One such methodology is viral genome reconstruction, which involves piecing together fragmented viral sequences from metagenomic datasets to reconstruct complete viral genomes. This task presents unique challenges due to the inherent complexity and variability of viral genomes and the diverse nature of metagenomic samples.
The "Unveiling Viruses" workshop offers a comprehensive exploration of viral metagenomics and viral genome reconstruction, providing participants with the skills and knowledge needed to navigate this exciting field. Tailored for PhD students and postdocs, it combines theoretical insights with hands-on practical sessions to equip attendees with essential tools and techniques.
Participants will embark on a two-part journey, beginning with a pre-workshop virtual session to familiarize them with key concepts and prerequisites. Through interactive discussions and live demonstrations, attendees will gain an understanding of metagenomics, its relevance in virology, and the importance of viral genome reconstruction in various contexts, including outbreak response and evolutionary studies.
Detalied planning
The two-part workshop delves into the exciting realm of metagenomics and equips you with the skills to reconstruct viral genomes directly from complex samples.
Part 1: Pre-workshop online session (1 hour)
Chose one of the two (identical) sessions where the attendees get technical help with their preparation before the hands-on workshop and a short introduction to the field. Attendance is mandatory for participation in part 2.
Part 2: Hands-on Workshop, Stockholm (2 hours)
Please note: Participants are strongly encouraged to attend the pre-workshop virtual session to ensure their Docker environment is set up and tested before the hands-on workshop. Additional details and resources will be provided closer to the workshop date.