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EMBO Practical Course

Genome sequencing, assembly, curation, and downstream analyses

08 – 12 September 2025 | Florence, Italy

  • Registration Deadline
  • 31 May 2025
  • Abstract Submission Deadline
  • 31 May 2025
  • Chosen Participants Will Be Notified By
  • 15 June 2025
  • Payment Deadline
  • 30 June 2025

Apply now!

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About the Practical Course

Practical Course illustration

Advances in long-read sequencing methods such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) and scaffolding approaches using chromosome conformation capture have significantly improved the possibility of generating chromosome-level assemblies for an increasing variety of organisms. As a consequence, the number of genome initiatives such as the Earth BioGenome Project, Darwin Tree of Life and the European Reference Genome Atlas are rapidly increasing to facilitate production of reference genomes as an essential tool in biodiversity and evolutionary biology research. The hands-on course in genome sequencing, assembly and downstream analysis will guide participants through main sequencing techniques and latest bioinformatic tools to produce high-quality genome assemblies of interest for downstream analysis and publication.

The course offers practical training in the use of computational tools for genome assembly such as HiFiasm, Verkko, Flye and NextDeNovo for PacBio HiFi reads or Flye, Canu, Raven and NextDeNovo for ONT reads, with troubleshooting sessions highlighting strengths and weaknesses of each methodology. Training and learning tools include a userfriendly dedicated Galaxy instance (https://usegalaxy.eu) through the Galaxy Training Infrastructure as a Service (TIaaS, https://usegalaxy.org/tiaas), which provides a GUI to run and analyse complex workflow. Students will be also trained in the use and interpretation of tools to perform Quality Control at each step of the genome assembly process and will participate in discussion on the quality of the results and possible strategies to improve the accuracy of assemblies. The course is aimed at graduate students and postdoctoral researchers as well as scientists at any stage of their careers.

Image credits: Nadège Guiglielmoni


About EMBO Courses and Workshops

EMBO Courses and Workshops are selected for their excellent scientific quality and timelines, provision of good networking activities for all participants and speaker gender diversity (at least 40% of speakers must be from the underrepresented gender).

Organisers are encouraged to implement measures to make the meeting environmentally more sustainable.

 

Speakers

 

Programme

 

Registration

  • Registration Deadline
  • 31 May 2025
  • Abstract Submission Deadline
  • 31 May 2025
  • Chosen Participants Will Be Notified By
  • 15 June 2025
  • Payment Deadline
  • 30 June 2025

 

  • STUDENT/POSTDOCS EUR 500
  • ACADEMIC EUR 750
  • INDUSTRY EUR 1,000

Registration includes:

  • Course registration

  • Course material

  • Accomodation

  • Meals and coffee breaks

  • Transportation (cards and/or bike rental)

  • Welcome dinner, group excursion

Payment

The selected participants will receive an e-mail with the attached acceptance letter together with payment details by 17 June 2024. Payments will be requested to be made through the University of Florence payment system.

Cancellation policy

We request that participants cancel on or before 30 June 2025. This will allow other participants who were not selected in the first place to attend the course.

Please note that we do not offer refunds unless the event is canceled for unforseen circumstances.

Selection criteria

Selection will be based on CVs and motivation letters of applicants. Priority will be given to (1) early stage researchers (i.e., PhD students and postdocs), (2) geographical balance favouring countries and institutions where genomic expertise is being or yet to be developed, (3) gender balance. Particular importance will be given to letters of motivation demonstrating that knowledge of genome assembly and downstream analyses is crucial to the applicant’s research and/or career. Multiple applications from the same research group are discouraged. Instead, we expect participants to share expertise acquired during the course with other members of their organization.

Please also provide at least one reference letter.

A working knowledge of the shell environment is highly recommendedbut it is not a prerequisite for selection. Selected applicants with no prior knowledge of command line tools should get acquainted with the shell environments by following the online tutorial prior to the course start date.

Abstract guidelines

In order to facilitate interactions between participants, the course will start, on the first day, with a poster session.
Posters should provide a general overview of each participant’s current research and have abstracts with a max. length of 250 words.

Poster specifications

Maximum poster size should be A0 format: 841 mm (width) x 1190 mm (height). A passport-style photograph of the presenting participant should be included in the upper-left corner of the poster.

Travel grants and registration fee waivers

Travel grants and registration fee waivers are available for participants.

Selection of awardees is handled directly by the organizers. EMBO travel grants and registration fee waivers are allocated on the basis of the quality of the submitted abstract.

Applicants do not need to apply separately for these but should indicate on the registration form if they wish to be considered.

Additional travel grants are available for EMBC Associate Member States Chile, India, Singapore and Taiwan.

Child care grants

EMBO Courses and Workshops offers grants to offset additional childcare costs incurred by participants or speakers when participating at any EMBO Courses and Workshop funded meeting. Eligible costs include fees for a caregiver or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please indicate on the registration form whether you would like to be considered for the grant. Please also describe how you intend to use the childcare grant and specify the sum that you will need.

Sustainability measures at this meeting

We strongly suggest traveling by tram from the city airport to reach the centre of Florence. Traffic limited zones make car access difficult in the historic centre of the town. The venue is 15-minute walking distance from the main train station and 10 min from the hotels where speakers and participants will be staying. There are several bike renting services as well as a Mobike bike sharing system in the city that can be used by participants.

Catering will be organized in local restaurants which use Tuscan ingredients, providing high quality food while reducing carbon footprint.

Abstract books and programs will be distributed in electronic formats only.


Code of conduct

Anti-harassment and non-discrimination policy

At EMBO, we believe that harassment and discriminatory behaviour are unacceptable in any setting.

Media and communications policy

Recording or communication of the presented data needs to be agreed upon by all concerned.

EMBO's code of conduct is applicable for all participants of this EMBO meeting and can be found here.

 

Contact

Claudio Ciofi
Email: claudio.ciofi@unifi.it

Camilla Reginatto De Pierri
Email: camilla.reginattodepierri@unifi.it

 

 

Venue

Venue images: Università degli Studi di Firenze

Santa Rosa School of Architecture
University of Florence
Via della Mattonaia 8
50121 Firenze
Italy

Accommodation

Speakers and students will be accommodated in regular single or double (single use) rooms. Hotels locations will be announced soon

The organisers will prepare the rooming list based on registration date after the payment deadline.

Transport

From the airport
Flights from the majority of European cities arrive at Florence international airport, which is just 20 minutes by tram to the main train station. From the train station, it takes approximately 15-minute walk, 10 minutes by public transport (bus 6, 14), or 5-10 minutes by taxi (for about 10 Euro) to get to the venue.

By train
Florence is a major high-speed railway hub with trains arriving regularly from the main Italian cities. From the train station, it takes approximately 15-minute walk, 10 minutes by public transport (bus 6, 14), or 5-10 minutes by taxi (for about 10 Euro) to get to the venue.

City bus
From the train station, it takes approximately 10 minutes by public transport (bus 6, 14) to get to the venue.

By taxi
A taxi ride from Florence international airport to the venue takes about 20 min for 25 Euro during weekdays and 28 Euro at weekends and on national holidays. From the main train station it takes 5-10 minutes for about 10 Euro.

About the Area

The venue is part of the University of Florence classrooms of Santa Teresa, located in the district of Sant’Ambrogio in the heart of Florence and within walking distant from the hotels where speakers and participants will be staying. Sant’Ambrogio has a vibrant day and night life. Main facilities and Florence historic sites are also at walking distance from the venue.

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