Metagenomic Bioinformatics Analysis

Toby Hodges   2020-02-18   Comments Off on Metagenomic Bioinformatics Analysis

Date/Time
Date(s) - 2020-02-18 - 2020-02-19
09:00 CET - 17:00 CET

Location
ATC Computer Training Lab, European Molecular Biology Laboratory (EMBL)

Categories


Instructors

  • Laura Carroll
  • Nicolai Karcher
  • Alessio Milanese
  • Jakob Wirbel
  • Georg Zeller

Introduction

Shotgun metagenomic sequencing approaches are being increasingly employed to characterize the human microbiome. Such complex metagenomics data sets are a rich source for generating functional hypotheses about the roles that gut microbiota play in human health and disease. In this bioinformatics course, participants will be exposed to computational and statistical approaches for the analysis of shotgun metagenomic data. Through a combination of theory-centric lectures and hands-on, practical exercises, the course will cover topics such as taxonomic profiling (i.e., determining “who’s there” in a microbial community), functional analysis (i.e., broadly assessing the functional and metabolic potential of a microbial community, and also mining for specific gene families such as toxins), and comparative metagenomics (i.e., identifying taxa or microbial functions associated with a disease of interest).

Course Synopsis

The course will cover the following topics:

  • Pre-processing and quality control of Illumina metagenomic data
  • Taxonomic profiling
  • Exploratory analyses and visualization methods for metagenomic data
  • Functional metagenomic profiling (using both general purpose databases and targeted approaches)
  • Comparative analysis of metagenomic data

Prerequisites

The following skills are required prerequisites for the course:

  • Familiarity with the Linux command line interface (e.g., running programs from the command line, creating and moving between directories, accessing a remote host via SSH)
  • Basic knowledge of the R programming language (e.g., loading data into R, manipulating data frames, creating basic plots)

Registration

A place on the course costs €150. After your registration is confirmed (see below), you will receive an invoice for the course fee.

Note: CRC 1371 members should choose the “CRC 1371 Place (CRC 1371 members only)” option below. All other registrants should choose “Standard Course Place.”

Please apply to attend the course by completing the form below. Shortly after applying, you will receive an email containing four short tasks to confirm that you have the prior knowledge of computing required to follow the course programme. These tasks should take no longer than 30 minutes to complete. Your registration will only be confirmed after these tasks have been completed. Full instructions will be included in the email sent after your application is received.

Contact

If you have any questions about the course, please contact the course organisers.

This workshop is sponsored by de.NBI, the German Network for Bioinformatics Infrastructure.

Bookings

Bookings are closed for this event.