Annotating & assembling genomes, commentary on the MAKER course by Jessika Samuels

Annotating and assembling genomes can be a daunting task for biologists. Navigating the command line, installing MAKER, mounting directoriess, working in Linux and Mother Nature could not keep these delegates from conquering and learning genome assembly and annotation using the MAKER software.

Professors Mark Yandell and Barry Moore facilitated a genome annotation and assembly workshop using the MAKER software from the 15th-19th September 2014. Held at the University of Pretoria’s Bioinformatics and Computational Biology Unit, the course was hosted by the African Centre for Gene Technologies and the Genomics Research Institute. The Department of Science and Technology co-sponsored the event by providing scholarships for participants from outside Pretoria as well as lunches for all participants.

Participants from all five ACGT partner institutions, ACGT affiliate the University of Limpopo and the University of the Western Cape participated in the 3 day course. The exuberant course presenters made learning the abstract content both easy and fun for participants.  These outstanding lectures were followed by hands-on data analysis sessions.

As an observer, not battling the command line during this course, it was heartening to see all the participants running their analyses and not giving up. Those command line “fundi’s” present assisted their fellow delegates with camaraderie and  patience I have not witnessed in a while. With all the positive attitude in the room, not even the blistering heat stopped the presenters and delegates running their analyses. Mark, Barry and Fourie were ever willing to lend a hand or fill the time while the analyses were running with some good coding humour. There were a lot of laughs, smiles and wide eyes as we continued throughout the three-day course.

On the 18th of September, course presenters assisted delegates in analysing their data and addressing any specific questions that were not addressed during the course. Prof Brenda Wingfield hosted Mark and Barry on the 19th of September, during which time members of her lab held group sessions with the presenters to discuss their projects.

Overall, the course was received positively by the delegates. The presenters were in turn suitably impressed by the level and enthusiasm of the delegates.

The workshop presented forms part of a series of bioinformatics training courses hosted by ACGT and its partners to address specific needs in bioinformatics skills training. For more information on upcoming bioinformatics training events, visit the events page on the ACGT website ( or like us on Facebook (