One of the major goals of ELIXIR-EXCELERATE task 10.3 (Capacity Building in Genome Assembly and Annotation) is to build capacity in genome assembly and annotation where it currently is insufficiently developed. We have organised five advanced level courses in five different countries. Teachers have been from four nodes (SE, BE, FR, NO). For each of the courses, the ELIXIR eLearning-platform developed by ELIXIR-SI within WP11 has been utilised. As a pilot for capacity building in new areas, an advanced course in single cell transcriptomics was held in Finland, Helsinki, May 27-29 2019. Eight countries were teaching at the course, which took the participants all the way from quality control to final results and also touched on related subjects such as spatial transcriptomics. Furthermore, we have created a good practices document, “10 steps to get started in genome assembly and annotation”, published in the F1000 ELIXIR gateway, a result of a year of work by 16 authors from 6 countries. It guides the reader all the way from early stages of a project, such as planning and DNA extraction, through analyses, to publication and submission of data following the FAIR principles. The publication has been extremely well received with the highest number of downloads of all publications in the ELIXIR gateway, and the second highest number of views (4169 downloads and 22126 views, as of 16 July 2019). The concept developed during ELIXIR-EXCELERATE for capacity building has proven excellent for genome assembly and annotation, and we have also applied it successfully for the new area single-cell transcriptomics. For sustainability, we conclude that capacity building in established areas will be performed as part of the ELIXIR Training platform activities, while capacity building in new areas will be using the mechanism of Implementation studies, where ELIXIR has regular calls for activities engaging multiple nodes. Implementation study funding can be used for a limited number of advanced courses for new areas. When these areas have matured, the capacity building activities will be included in the ELIXIR Training platform.