Section outline

  • Announcements and Communication tools

    Collapse all Expand all

    Dear participant,

    welcome to the First Hands-on Workshop on Marine Metagenomics. Hope you will enjoy all five days of the workshop.

    DON'T FORGET THE FEEDBACK SURVEY

    • Announcements Forum
    • Discussion forum

      Students´ questions to teachers and other students are posted and answered here.

    • Chat room

      Live chat for live comments and questions during the course.

  • Venue and transportation

    The course will take place at the Arctic University of Norway in Tromsø.

    • Time schedule URL
    • Classroom location URL

      Teorifagbygget Hus 1, Floor 4, room 1433

    • Timetable of airport shuttles URL

      Bus from the airport:

      Airport (Langnes Lufthavn) - City center (Sentrum)
      Airport (Langnes Lufthavn) - University (UIT/ISV) and University Hospital (UNN - Universitetssykehuset)

      Bus to the airport:

      City center (Sentrum) - Airport (Langnes Lufthavn)
      University (UIT/ISV) and University Hospital (UNN - Universitetssykehuset) - Airport (Langnes Lufthavn)

    • The bus system in Tromso URL
    • Map of Tromso bus lines URL

      University = "UiT/UNN"
      City center = "Sentrum"

    • Location of the course dinner URL

      Monday Nov. 26, 18:00, Science Park - Siva innovasjonssenter

    • Group photos Folder

      Group photos of course participants

  • Introduction to Linux Command Line

    Just a gentle suggestion

    Dear participants, the entry condition for the Hands-on workshop in Marine Metagenomics is a working knowledge of Unix/Linux command line. In case you want to refresh this knowledge you can browse through slides in the Unix/Linux Tutorial for Beginners 2 and use the exercises as well. This course, which is not a part of the MM workshop, was prepared and led by Michaela Martis and her co-workers from ELIXIR Sweden in collaboration with ELIXIR Slovenia and she kindly allowed us to use it here too. We believe that mainly slides and exercises from the 2nd part of Session 1 and slides from Sessions 2 & 3 could be beneficial for our purpose.

  • Deployment script for tool installation

    For those for you who would like to continue using the marine metagenomics tools, Espen Jr. wrote a deployment script which installs all the tools on your Linux server or VM. Below is the link to the deployment script on Espen Jr's GitHub page. Please read the instructions before running the script.

  • Group work - Friday

    On Friday, Nov. 30 you will get the chance to apply the skills you have acquired during the this week. You will work in 5 groups - each group is given a dataset. The task is to analyse the data and present the result to all course participants at the end of the day.

  • Day 1 - Monday, 26th November

  • Day 2 - Tuesday, 27th November

    • 09:00 - 09:30

      Summary day 1

    • 09:30 – 10:00

      ELIXIR - A distributed infrastructure for life-science information (Nils)

    • Lecture: ELIXIR - A distributed infrastructure File

    • 10:00 - 10:30    Coffee break

    • 10:30 – 11:30

      META-pipe analyses platform (Espen J)

    • Lecture: META-pipe analysis pipeline File

    • 11:30 – 12:30

      Assembly & validation (Erik)

    • Lecture: Assembly and validation File

    • 12:30 – 13:30    Lunch

    • 13:30 - 18:00

      Hands on - Quality control, filtering, assembly and validation

    • Exercise: Quality control, filtering, assembly and validation File

    • 16:00 – 16:30    Coffee break

  • Day 3 - Wednesday, 28th November

    • 09:00 - 09:30

      Summary day 2

    • 09:30 – 10:30

      Taxonomic classification of metagenomics samples (Erik)

    • Lecture: Taxonomy File

    • 10:30 - 11:00    Coffee break

    • 11:00 – 11:30

      New data resources for marine metagenomics (Nils)

    • Lecture: New marine data resources File

    • 11:30 – 12:30

      Hands on - Taxonomic classification and functional assignment

    • Exercise: Taxonomic profiling File
    • Exercise: Functional assignment File

      This exercises includes submission of jobs to META-pipe

      Location of preprocessed files (META-pipe results) in VMs:

      /practical/4/preprocessed.tar.gz

      How to decompress the preprocessed files with META-pipe results:

      cd /practical/4

      tar -xzvf preprocessed.tar.gz

      Open Artemis by typing:

      art

      in the terminal

    • 12:30 – 13:30    Lunch

    • 13:30 – 15:30

      Hands on - Taxonomic classification and functional assignment (cont.)

    • 15:30 – 16:00    Coffee break

    • 16:00 - 18:00

      Hands-on - Taxonomic classification and functional assignment (cont.)

  • Day 4 - Thursday, 29th November

    • 09:00 - 09:30

      Summary day 3

    • 09:30 – 10:30

      Hands on: Taxonomy-independent binning from reads and contigs

    • Exercise: Taxonomy-independent binning from reads and contigs File

    • 10:30 - 11:00    Coffee break

    • 11:00 – 12:30

      Hands on: Taxonomy-independent binning from reads and contigs (cont.)

    • 12:30 – 13:30    Lunch

    • 13:30 - 15:00

      Hands on: Taxonomy-independent binning from reads and contigs  (cont.)

    • 15:00 - 15:30

      Comparative metagenomics (Espen J)

    • Presentation: Challenges in comparative metagenomics File

    • 15:30 - 16:00    Coffee break

    • 16:00 – 18:00

      Hands on - Comparative metagenomics (All)

    • Exercise: Visualization of data & comparative metagenomics File

      To start MEGAN, type:

      /opt/SfB-course/megan/MEGAN

      in the terminal

  • Day 5 - Friday, 30th November

    • 09:00 - 09:30

      Summary day 4

    • 09:30 – 12:00

      Group work in 5 groups

      After copying files to your home directory, go to your home directory and change permissions with the chmod command:

      cd ~

      chmod -R a+w <name-of-copied-directory>

    • List of groups and their members File
    • Exercise: Group work File

    • 10:30 - 11:00    Coffee break

    • 12:00 – 12:30    Lunch

    • 12:30 – 14:00

      Presentation of group work results

    • 14:00 – 14:30    Coffee break and group photo