A Practical Workshop will be held during 7-11 May 2018, in Oeiras, hosted by the Portuguese ELIXIR Node in cooperation with the nodes involved in ELIXIR-EXCELERATE Workpackage 6 “Marine Metagenomics”.
Program: [Link to All Material]
Day 0 - Monday May 7
09:30 - 10:00: Welcome and round of presentation by participants (Daniel Sobral, Belén Carbonetto, Pedro Fernandes).
10:00 - 10:30: Introduction to NGS (Daniel Sobral / Belen Carbonetto)
10:30 - 11:00: cofee break
11:00 - 12:00: Introduction to 16S Metagenomics (Daniel Sobral / Belen Carbonetto)
12:00 - 13:00: Introduction to Linux command line (Daniel Sobral / Belen Carbonetto / Pedro Fernandes)
13:00 - 14:00: Lunch
14:00 - 18:00: 16S Metagenomics data analysis using Qiime2 (Belen Carbonetto / Daniel Sobral) [Link to data and scripts]
16:00 - 16:30 cofee break
Day 1 - Tuesday May 8
09:30 - 09:45: Welcome to the Workshop (Daniel Sobral)
09:45 - 10:00: ELIXIR - A distributed infrastructure for life-science information (Nils Willassen)
10:00 - 10:30: Introduction to metagenomics (Nils Willassen)
10:30 - 11:00: cofee break
11:00 - 11:30: The metagenomics data life-cycle: standards and best practice (Nils Willassen)
11:30 - 12:15: Sequencing technologies for metagenomics (Espen Åberg)
12:15 - 13:00: META-pipe analyses platform (Espen Robertsen)
13:00 - 14:00: Lunch
14:00 - 14:15: Quality control, filtering, assembly & validation (Erik Hjerde)
14:15 - 14:30: Introduction to Hands on - Quality control, filtering, assembly & validation (Erik Hjerde)
14:30 - 18:00: Hands on - Quality control, filtering, assembly & validation [Answers] (Hjerde/Robertsen/Åberg)
16:00 - 16.30: coffee break
Day 2 - Wednesday May 9
09:30 - 10:30: Taxonomic classification (Erik Hjerde)
10:30 - 11:00: coffee break
11:00 - 12:30: Hands on - Taxonomic classification & functional assignment [Answers] (Hjerde/Robertsen/Åberg)
12:30 - 13:30: Lunch
14:00 - 15:00: (cont.) Hands on - Taxonomic classification & functional assignment [Answers] (Hjerde/Robertsen/Åberg)
15:00 - 15:30: New data resources for marine metagenomics (Nils Willassen)
16:00 - 16:30: coffee break
16:30 - 18:00: Functional assignment (Erik Hjerde)
Day 3 - Thursday May 10
09:30 - 10:00: Genome assembly from metagenomic reads - MAG (Erik Hjerde)
10:30 - 11:00: coffee break
11:00 - 12:30: Hands on - MAG [Answers] (Hjerde/Robertsen/Åberg)
12:30 - 13:30: Lunch
13:30 - 16:00: Comparative metagenomics (Espen Robertsen)
16.00 - 16.30: coffee break
13.30 - 18.00: Hands on - Visualization of data & comparative metagenomics [Answers] (Hjerde/Robertsen/Åberg)
Day 4 - Friday May 11
09:30 - 10:30: Case Study (Ricardo Leite)
10:30 - 11:00: coffee break
11:00 - 12:00: Case Study (Rodrigo Costa): The microbiome of keratose marine sponges: diversity, function and biotechnology
12:00 - 13:00: Lunch
13:00 - 14:00: Case Study (Pedro Santos)
14:00 - 16:00: Open session - Discuss participants projects (selected talks from participants)
16:00 - 16:30: coffee break
16:30 - 17:00: Wrap-Up
Registration: Participation is free of charge but requires registration by using this google form.
We will accept only a maximum of 20 participants. Preference will be given to those currently directly involved in metagenomic projects, so please indicate a brief description of your project(s) in the application. Please indicate in the application form your experience with running bioinformatic tools.
Lecturers:
Belén Carbonetto
Affiliation: Instituto Gulbenkian de Ciência, Portugal
Erik Hjerde
Affiliation: UiT, Tromsø, Norway
Nils Willassen
Affiliation: UiT, Tromsø, Norway
Espen Åberg
Affiliation: UiT, Tromsø, Norway
Espen Robertsen
Affiliation: UiT, Tromsø, Norway
Elixir-PT Hosts:
Pedro Fernandes
Affiliation: IGC, Oeiras, PT
Daniel Sobral
Affiliation: IGC, Oeiras, PT
Partnership: INCD
Contact: For any questions about this course, please contact Daniel Sobral (e-mail address below)
Instituto Gulbenkian de Ciencia
Rua da Quinta Grande, 6
2780-156 Oeiras
Portugal