Workshop on Genome Assembly and Annotation

A course will be held in Oeiras, hosted by the Portuguese ELIXIR Node in cooperation with the nodes involved in ELIXIR-EXCELERATE task 10.3 “Capacity Building in Genome Assembly and Annotation”.


The course is aimed at researchers interested in learning more about genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue step-by-step to describe all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using command line Linux. After the course the participants will be aware of common practices and commonly used tools and be able to run assembly and annotation projects on their own.




  • Pedro Fernandes graduated in Electronics and Telecommunications Engineering at IST (U.T. Lisboa). He worked in Biomedical Engineering, Biophysics and Physiology and changed to Bioinformatics in 1990. He established the first user community in Portugal around the national service provided by the portuguese node of the EMBnet. In 1998 he created the Gulbenkian Training Programme in Bioinformatics, that provided user skills to more than 3200 course attendees throughout its twelve years of existance. In 2002, in cooperation with Mario Silva from FCUL, he designed a graduate Programme in Bioinformatics. He currently teaches Bioinformatics both in graduate and undergraduate programmes. 

           Affiliation: Instituto Gulbenkian de Ciência, Oeiras, PT



  • Daniel Sobral graduated in Informatics Engineering from Instituto Superior Técnico (Lisbon, Portugal). His interest in Biology led him to join the Gulbenkian PhD programme, and conduct his doctoral studies in Bioinformatics at the Université Aix-Marseille (France) with Dr. Patrick Lemaire. During his PhD he worked in different aspects of bioinformatics, particularly focusing on gene expression networks underlying embryonic development of a model organism, all of this integrated into a community resource. Later he became a Developer for the Ensembl Project where he worked mostly in integrating epigenetic data from the ENCODE project in Ensembl. In this context he gained significant experience with high throuthput sequencing data. In 2012 he moved back to Portugal, where he joined the Bioinformatics Unit at the IGC to assist the local research community in handling the sequencing revolution brought about by high throughput technologies. Within this role he been collaborating in several projects, ranging from genomics, transcriptomics and epigenetics. He has become the Head of the Bioinformatics Unit at IGC since 2014.  

           Affiliation: Instituto Gulbenkian de Ciência, Oeiras, PT


Program: A final agenda will be added here closer to the date of the course.

You can find here an agenda of a previous workshop in Slovenia.


Registration: Participation is free of charge but requires registration.


Register using this google form until August the 30th


We will accept only a maximum of 30 participants. Preference will be given to those currently directly involved in genomic projects, so please indicate a brief description of your project(s) in the application. Given that most practical exercises require the linux command-line, preference will be given to those that have minimal experience with running tools in the command-line. Please indicate in the application form your experience with running bioinformatic tools.

If you require assistance in finding accommodation, please indicate that in the application form.


Contact: For any questions about this course, please contact Daniel Sobral (e-mail address below)

Start date: 
End date: 
Instituto Gulbenkian de Ciência
R. Q.ta Grande 6
2780-156 Oeiras
Daniel Sobral
Event type: 
Workshops and courses