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:​

 

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)

 

Start date: 
2018-05-07
End date: 
2018-05-11
Location: 
Instituto Gulbenkian de Ciencia
Rua da Quinta Grande, 6
2780-156 Oeiras
Portugal
PT
Name: 
Daniel Sobral
Event type: 
Workshops and courses
Topic: