Course at EMBL-EBI

Metagenomics bioinformatics

This course will cover the use of publicly available resources to manage, share, analyse and interpret metagenomics data, including marker gene, whole gene shotgun (WGS) and assembly-based approaches. Delegates will gain hands-on experience using a range of data resources and tools, interspersed with lectures. Additionally, there will be the opportunity to discuss the challenges facing researchers in the field.

Who is this course for?

This course is aimed at life scientists who are working in the field of metagenomics, in the early stages of their data analysis, and who may already have some prior experience in using bioinformatics in their research.

Prerequisites

Some practical sessions in the course require a basic understanding of the Unix command line and the R statistics package. If you are not already familiar with these then please ensure that you complete these free tutorials before you attend the course:

What will I learn?

Learning outcomes

After this course you should be able to:

  • Submit data to public resources for metagenomics
  • Interpret results and compare with other metagenomics datasets
  • Use a range of tools to perform some data analyses
  • Discuss the pitfalls and challenges in the field

Course content

During this course you will learn about:

  • Data generation: Next Generation Sequencing, amplicon approaches (ribosomal  RNA), whole genome shotgun (WGS) approaches, assembly and metagenome assembled genomes (MAGs)
  • Data analysis: MGnify, HMMER, InterPro, GO, FASTQC, metabolic and pathway analyses
  • Data standards and submission: European Nucleotide Archive (ENA), Genomic Standards Consortium (GSC), SRA, Webin
  • Public resources for metagenomics

Trainers

Rob Finn
EMBL-EBI, UK
Alex Mitchell
EMBL-EBI, UK
Darren Wilkinson
University of Newcastle, UK
Chris Quince
Warwick Medical School, UK
Lorna Richardson
EMBL-EBI, UK
Josephine Burgin
EMBL-EBI, UK
Sam Holt
EMBL-EBI, UK
Amanda Warr
University of Edinburgh, UK
Alexandre Almeida
EMBL-EBI, UK
Guillermo Rangel
EMBL-EBI, UK
This course has ended

10 - 13 June 2019
European Bioinformatics Institute
United Kingdom
£580
Contact
Meredith Willmott

Organisers
  • Rob Finn
    EMBL-EBI, UK
  • Alex Mitchell
    EMBL-EBI, UK
  • Alexandra Holinski
    EMBL-EBI, UK

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