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

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

Monday - 1 July

09:00 - 10:00 Lecture Henrik Lantz Introduction and genome properties
10:00 - 11:00 Lecture Christophe Klopp Quality control of sequence data
11:00 - 12:00 Practical Christophe Klopp Quality control of sequence data
12:00 - 13:00 Lunch break
13:00 - 14:00 Practical Christophe Klopp Quality control of sequence data
14:00 - 15:00 Lecture Tomas Larsson Genome assembly using Illumina data
15:00 - 17:00 Practical Tomas Larsson Genome assembly using Illumina data

Tuesday - 2 July

09:00 - 10:00 Lecture Christophe Klopp Long read (PacBio, Nanopore) genome assembly
10:00 - 12:00 Practical Christophe Klopp Long read (PacBio, Nanopore) genome assembly
12:00 - 13:00 Lunch break
13:00 - 14:00 Lecture Tomas Larsson Assembly validation
14:00 - 17:00 Practical Tomas Larsson Assembly validation

Wednesday - 3 July

09:00 - 17:00 Discussion & hands-on Participants & trainers Discussion of the participants’ own projects (also hands-on work if possible), and catch-up session of day 1 and 2 for those that did not have time to finish the practicals.

Thursday - 4 July

09:00 - 10:00 Lecture Joelle Amselem Transposable element annotation
10:00 - 12:00 Practical Joelle Amselem Transposable element annotation
12:00 - 13:00 Lunch break
13:00 - 14:00 Lecture Jacques Dainat Structural annotation
14:00 - 17:00 Practical Jacques Dainat Structural annotation

Friday - 5 July

09:00 - 11:00 Practical Jacques Dainat Structural annotation
11:00 - 12:00 Lecture Lucile Soler Functional annotation
12:00 - 13:00 Lunch break
13:00 - 14:30 Practical Lucile Soler Functional annotation
14:30 - 16:00 Lecture & Practical Lucile Soler Prokaryote annotation
16:00 - 17:00 Wrap-up and feedback session



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 SanitĂ  (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