GTPB|AM22 - Applied Metagenomics 2022

DESCRIPTION

This course will give a comprehensive introduction to the research field of metagenomics. It will cover the basic concepts of microbiome analysis of shotgun metagenomic data using state of the art bioinformatics (amplicon sequencing will not be covered). The analysis methods that are being introduced are generic for all types of microbiomes, but we will be using data from the human microbiome as showcases. The course will start with the main preprocessing steps of raw sequence data, before various downstream analysis will be covered separately. These include taxonomic analysis, assembly, binning, and finally functional analysis with focus on antibiotic resistance genes. The theoretical part for each topic will be introduced via lectures, followed by practical hands-on exercises.

LEARNING OBJECTIVES

The participants will have acquired a theoretical basis and practical experience to understand the basic concepts of metagenomic analysis in order to conduct academic studies related to microbiome samples. This includes:

• performing advanced downstream analysis on both taxonomic functional profiles
• performing quality control, assembly and binning of metagenomic sequence data
• performing functional analysis and resistome analysis of metagenomes

INSTRUCTORS

Erik Hjerde has a background in biology with a PhD in Genomics. During his career he has been working mainly with prokaryotes with focus on genomics and transcriptomics. In the last years, the focus has moved more towards metagenomic analysis on communities from both the human host as well as from various ecological habitats. He is the head of one national (Norwegian) work package within ELIXIR, that focuses on providing bioinformatic end user support and training. Affiliation: ELIXIR-NO, University of Tromsø, Tromsø, NO

Espen Robertson has a background in biology with a PhD in Metagenomics. While still doing some metagenomic research, his main focus recently has been database integrations and software development. Espen is involved in various ELIXIR projects involving sensitive data, pipeline prototyping, administration of the useglaxy.no project and various other topics. Affiliation: ELIXIR-NO, University of Tromsø, Tromsø, NO

TARGET AUDIENCE

The course is intended for researchers and students that are working or are planning to work with data analysis of metagenomic data.

CAPACITY

20 participants

IMPORTANT DATES

Deadline for applications: October 3^rd 2022

Course date: October 10^th - October 14^th 2022

APPLICATION

More details about this course, including application instructions, are available at http://gtpb.igc.gulbenkian.pt/bicourses/2022/AM22/