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EMBO Practical Course

Hands-on course in genome sequencing, assembly, and downstream analyses

28 January – 03 February 2024 | Valencia, Spain

  • Registration & Abstract Submission Deadline
  • 28 September 2023
  • Chosen Participants Will Be Notified By
  • 28 October 2023
  • Payment Deadline
  • 28 November 2023

Apply now!

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About the Practical Course

The field of genome assembly has been revolutionized by the availability of long reads (Nanopore, PacBio) and scaffolding approaches using chromosome conformation capture (HiC), making it possible to generate chromosome-scale assemblies for virtually any organism. This practical course will focus on these developments, with the aim of equipping each participant with the theoretical knowledge and practical know-how to be able to sequence their genome of interest and analyze it, all the way to publication. Reference genomes are becoming a new fundamental tool in biodiversity and evolutionary research and accordingly, the number of reference genome initiatives is rising, as exemplified by the growing number of international initiatives aimed at increasing the availability of genomes across the tree of life such as the Earth BioGenome Project.

The course includes practical training in the use of computational tools for genome assemblies such as HiFiasm, Flye, as well as NextDeNovo and for genome annotation such as GeMoMa, Braker, and Maker. The strengths and weaknesses of each of them will be discussed after its use. More importantly, the students will be trained in the use and interpretation of tools to perform Quality Control (QC) at each step, allowing them to discuss the quality of the results and possible strategies to resolve assembly problems and increase the quality of the assemblies.

The course is aimed at graduate students and postdoctoral researchers, but applications from scientists at any stage of their careers are encouraged.

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.







  • Registration & Abstract Submission Deadline
  • 28 September 2023
  • Chosen Participants Will Be Notified By
  • 28 October 2023
  • Payment Deadline
  • 28 November 2023



Registration includes:

  • Course registration

  • Course material

  • Accommodation

  • Lunches, dinner, coffee breaks

  • Transportation (cards and/or bike rental)

  • Welcome dinner, group excursion, social events


The selected participants will receive an e-mail with the acceptance letter together with information and details regarding the payment procedure on 28 September 2023. Payments will be made through UPV payment system.

Selection criteria

Selection will be based on the CVs and motivation letters of the applications, with the aims of favouring

  1. early-stage researchers (i.e., PhD students and postdocs)
  2. balanced geographical origin with an emphasis on countries and institutions where genomic expertise is currently scarce
  3. gender balance

Applicants who demonstrate in their motivation letter that knowledge of genome assembly and downstream analyses is important for their short-term research and/or career plans will be favoured.

Multiple applications from the same group are discouraged - instead, we expect participants to share with the other members of their groups the knowledge and know-how they will have acquired during the course.

A working knowledge of the shell environment will be required by the beginning of the course but 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 arriving in Valencia.

Abstract guidelines

In order to facilitate interactions between participants, the course will start with a poster session on the first day. Posters should provide a general overview of each participant’s present research, with abstracts less than 300 words in length.

Poster specifications

Maximum poster size (A0 format) - 841 mm (width) x 1189 mm (height). A passport-style photograph of the presenting participant should be included in the upper-left corner of each 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.

Special travel grants and registration fee waivers

A limited number of travel grants and registration fee waivers are availablefor scientists working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia and Turkey. Grants are allocated on the basis of the quality of the submitted abstract.

A maximum of 700 Euros per participant are available to cover registration fees, travel, and accommodation (no additional subsistence costs can be covered). To apply, please indicate the itemized amount requested in the travel grants section of the registration form.

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.


This meeting is implementing several sustainability efforts, covering the cost of bike rentals and public transport for our participants, avoiding the use of plastic in badges, plastic water bottles and other plastic disposable material for the course and promoting initiatives like no-meat Monday.

Participants travelling by train should indicate this to the organisers to receive a discount.

Code of conduct

Anti-harassment and non-discrimination policy

At EMBO, we believe that harassment and discriminatory behaviour are unacceptable in any setting. EMBO's code of conduct is applicable for all participants of this EMBO meeting and can be found here.



Silvia Manrique





Nexus Building
Valencia Polytechnic University (UPV)
Camí de Vera
Valencia, Spain


Everybody, including speakers, organisers, and students, will be accommodated in the same hotel (Hotel Silken-Puerta Valencia, Avinguda del Cardenal Benlloch, 28, 46021 València, Spain). The 30 students will be accommodated in 30 double rooms (single use). The organisers will prepare the rooming list (based on the registration date of the participants, their accommodation wishes, and their gender) right after the payment deadline.


By plane

Valencia Airport is located in the nearby town of Manises, about 8 km away from the city. Flights arriving from major Spanish and European cities land there.

  1. By taxi
    You can catch a taxi from Manises to the University; the journey takes about 25 minutes.
  2. Underground
    At the airport, you can take line 3 (heading to Rafelbunyol), get off at Benimaclet, and switch to line 4 (heading to Doctor Lluch). The second stop leaves you in front of the Universitat Politècnica de València.
  3. City Bus
    You can take the bus 150 Valencia-Airport: its itinerary is Airport-Manises-Quart de Poblet-Mislata-Valencia. In the city of Valencia, you have stops on Cid Avenue, Cuenca Street, 'Gran Vía' Fernando el Católico and Pío XII Avenue. From any of these bus stops, you can take a bus or the underground to the University. Undoubtedly, the best option is to get off at the Avenida del Cid and walk to the underground station (Avenida del Cid) entrance. Take line 3 (towards Rafelbunyol), get off at the 6th stop (Benimaclet) and change to line 4 (towards Doctor Lluch). The second stop drops you off at the UPV entrance.

By train

Valencia has two train stations that are quite close, with different routes: Joaquín Sorolla Station and Valencia North Train Station. Joaquín Sorolla Station has the following long-distance routes: Madrid, Barcelona, Alicante, Castellón and Albacete. All other long-distance, middle-distance and suburban routes leave from Valencia North Train Station. The distance between the two stations can be covered on foot in 10 minutes or by an exclusive Renfe bus, which is free when you show your train ticket. Both stations are located in the middle of the city.

  1. City bus
    From Joaquín Sorolla Station, you can take bus number 9 to go to Universitat Politècnica de València. The stop is on San Vicente Mártir Street. From the North Train Station, you can take number 40. The stop is on Alicante Street.
  2. Underground
    Next to Joaquín Sorolla Station, you have the underground station of the same name. You must take line 5 (heading to Marítim-Serreria or Neptú), get off at the fourth stop (Alameda), switch to line 3 (heading to Rafelbunyol), get off at the second stop (Benimaclet), and switch to line 4 (heading to Doctor Lluch). The second stop leaves you in front of the university. From the North Train Station, the journey is shorter, since you need a switch less. In front of the North Train Station, you can find an underground station (Xàtiva). You must take line 3 (heading to Rafelbunyol), get off at the fourth stop (Benimaclet), and switch to line 4 (heading to Doctor Lluch). Get off at the second stop and you are already at the UPV.

About the Area

The practical course will be organized at the campus of the Vera of the Universitat Politècnica de València, with a vibrant student life. The popular neighborhood of Cabanyal as well as the Malvarrosa beach are just within walking distance. The campus is well connected with the Valencia city center with several cultural attractions such as the City Hall, the Cathedral, the Botanical Garden, the Central Market, and the old city Gates of Serrano and Quart.

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