Metagenomics Bioinformatics 2019

Date:

 Monday 10 Thursday 13 June 2019

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom

Application opens: 

Monday 17 December 2018

Application deadline: 

Friday 22 March 2019

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£720 - (Including Accommodation)

Overview

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.

Audience

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:

 

Syllabus, tools and resources

During this course you will learn about:

  • Data generation: Next Generation Sequencing, amplicon-based approaches (ribosomal  RNA), WGS, assembly
  • 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

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

Programme

Please note: This is a provisional programme and changes are still possible. A final version will be published soon. 

Time Topic  
Day 1 - Monday 10 June 2019
11:30 - 12:30 Registration and lunch  
12:30 - 13:00 An Introduction to the EBI  
13:00 - 13:30 Sequencing technologies for metagenomics   
13:30 - 14:00 Introduction to metagenomics data analysis: why provenance matters  
14:00 - 15:00 Quality control   
15:00 - 15:30 Tea/coffee break  
15:30 - 17:00 Markers, reference databases and genes for taxonomic analysis  
17:00 - 17:30 Free time   
17:30  Dinner  
Day 2 - Tuesday 11 June 2019
09:00 - 10:30 to be confirmed  
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 to be confirmed  
12:00 - 13:00 Lunch  
13:00 - 15:00 EBI metagenomics with hands on    
15:00 - 15:30 Tea/coffee break   
15:30 - 17:30 EBI metagenomics with hands on (ctd)  
17:30 - 18:00  Free time  
18:00  Dinner  
Day 3 - Wednesday 12 June 2019
09:00 - 10:30 Sequence and metadata submission ENA  
10:30 - 11:00 Tea/coffee break  
11:00 - 11:30 Other analysis platforms  
11:30 - 12:30 Searching the metagenomics peptide database  
12:30 - 14:00 Lunch and poster session   
14:00 - 15:30 Assembly and binning with hands-on  
15:30 - 16:00 Break   
16:00 - 17:30 to be confirmed  
17:30 Free time  
18:00 Dinner  
Day 4 - Thursday 13 June 2019
09:00 - 10:00 to be confirmed  
10:00 - 11:00 to be confirmed  
11:00 - 11:30 Tea/coffee break   
11:30 - 13:00 to be confirmed  
13:00 - 13:30 Course feedback and wrap up   
13:30 Lunch  
14:15 Coach departs for Cambridge train station