IMPORTANT DATES

• Deadline for applications: 10 May 2019
• Chosen participants will be notified by: 17 May 2019
• Course date: 1-5 July 2019
  
  

VENUE
University of Milano-Bicocca
Lab. 715, U7 Building (link to the map)
via Bicocca degli Arcimboldi, 8
20126 Milano, Italy

Accommodation
Suggested hotels are Starhotel Tourist and Hotel Arcimboldi, which are both within a 10-minute walk from the course venue.

FEE
The course does not include a fee, but the participants are expected to pay their own travel and accomodation costs (if any).

SELECTION
A maximum of 24 candidates will be selected based on their need for the course as emerging from the application form. Chosen participants will be notified by 17th May 2019. Priority will be given to candidates from ELIXIR-IIB member institutes (see the list at the bottom) and ELIXIR Nodes.
Go to the Application Form - Registration.

Cancellation policy: Attendance is limited to 24 participants. We expect many more applications. Accepted participants commit to attend the course for its whole duration. Failure to attend training sessions is disruptive. Moreover, it blocks other candidates from participating. Therefore, a cancellation policy is in place so that only written requests presented 10 days in advance relatively to the course starting date are accepted.

Instructors

• Henrik Lantz - ELIXIR-SE
• Jacques Dainat - ELIXIR-SE
• Lucile Soler - ELIXIR-SE
• Tomas Larsson - ELIXIR-SE
• Christophe Klopp - ELIXIR-FR
• Joelle Amselem - ELIXIR-FR
  
  

Organisers

• Henrik Lantz - ELIXIR-SE
• Gianluca Della Vedova - ELIXIR-IT (Local Organiser) - Univ. of Milano-Bicocca
• Brane L. Leskosek - ELIXIR-SI
• Loredana Le Pera - ELIXIR-IT (Training Coordinator Deputy) - CNR-IBPM/CNR-IBIOM
• Allegra Via - ELIXIR-IT (Training Coordinator) - CNR-IBPM
  
  

Contact

For all kinds of queries, please contact the local organiser Gianluca Della Vedova at: gianluca.dellavedova@unimib.it. For questions about course content, please contact Henrik Lantz at: henrik.lantz@nbis.se.

Course Description

The course will take the participants through all steps of a genome assembly and annotation project, starting with quality control, moving into genome assembly and assembly validation, and ending with structural and functional annotation. Both short and long read technologies will be discussed, as well as supporting technologies. Lectures are mixed with practicals, with a majority of the time spent doing hands-on analyses in the command terminal. Focus is on eukaryotes, although most methods will be applicable to any organism. One day is set aside to discuss the participants own projects, and work with that data, if available.

Target audience

This course is aimed at PhD-students, post docs or other researchers interested in learning about genome assembly and genome annotation. It will be especially useful for researchers that have (or will have) data of their own and want run the assembly - and annotation - tools themselves.

Learning outcomes

By the end of this course, learners will be independently able to:

• Understand how genome properties will influence a genome assembly and annotation project
• Set up a workflow for a genome assembly and annotation project
• Perform quality control of Illumina data and check data integrity
• Perform genome assembly using Illumina, PacBio, and Nanopore reads
• Compare assemblies and check them for mis-assemblies and contamination
• Perform basic annotation of transposable elements
• Perform structural annotation of prokaryote and eukaryote genomes
• Assign functional information to structurally annotated genes
  
  

Course prerequisites

The participants will need to have some experience in Linux command line (bash), enough to start tools and find paths to files. Experience with Next Generation Sequencing data and common file formats (fasta, fastq, bam, etc.) will be very useful, but is not mandatory.

Application Form - Registration

After selection, confirmed participants will be able to access the course agenda, materials and communication tools on the ELIXIR-SI eLearning Platform (EeLP).

Programme

ELIXIR-IIB member institutes

1. CNR, National Research Council (Lead Institute)
2. CRS4
3. CINECA
4. Edmund Mach Foundation, Trento
5. ENEA
6. Fondazione Telethon
7. INFN
8. Istituto Superiore di Sanità (ISS)
9. GARR
10. Stazione Zoologica Anton Dohrn, Napoli
11. University of Roma "Sapienza"
12. University of Bari
13. University of Bologna
14. University of Firenze
15. University of Milano
16. University of Milano Bicocca
17. University of Napoli
18. University of Padova
19. University of Parma
20. University of Roma "Tor Vergata"
21. University of Salerno
22. University of Torino
23. University of Tuscia