ELIXIR-EXCELERATE Workshop on Marine Metagenomics

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: