layout	title	date_start	date_end	venue	description
post	Pangenomics <font color='green'>[open]</font>	2019-12-14	2019-12-18	virtual	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.

IMPORTANT DATES

• Deadline for applications: 30 October 2020
• Chosen participants will be notified by: 6 November 2020
• Course date: 14-18 December 2020

VENUE

This training will take place online. The instructors will provide you with the information you will need to connect to this event.

FEE

The course does not include any fee.

SELECTION

A maximum of 20 candidates will be selected based on their need for the course as emerging from the application form. Chosen participants will be notified by 6th November 2020. 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 20 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

• Erik Garrison - University of California Santa Cruz

Helpers

• Flavia Villani - University of California Santa Cruz
• Simon Heumos - afflilation
• Andrea Guarracino - affiliation

Organizers

• Vincenza Colonna - ELIXIR-IT
• 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 about the course, please contact Erik Garrison at erik.garrison@ucsc.edu.

Course Description

The course will take the participants through all steps of a pangenome construction and analysis process. We will learn the basic principles and key algorithms of contemporary pangenomic methods based on pangenome graphs. At the end of the course, participants will be able to design and complete their own pangenomic analyses.

Lectures will provide background for the work, but this is a practical course, with a majority of the time spent doing hands-on analyses on the command line. To keep analysis times short and encourage interative exploration, we will tend to focus on organisms with smaller genomes, but the techniques we will use are scalable and applicable to any organism. Participants are encouraged to bring their own data, and time will be allocated to discuss and test the application of pangenomic methods to these data.

Target audience

This course is aimed at PhD students, postdocs 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

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 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