Course Location: Evolutionsbiologiskt Centrum (EBC), Uppsala

The course on Best Practices for Reference Genome Generation covers essential topics from project planning and sample collection to sequencing, data processing, data mobilization and deposition in open repositories.

Register here!

Target audience

The course is designed for junior and senior researchers utilizing reference genomes for biodiversity genetics research.

Topics and Instructors

• Nagoya Protocol & ABS requirements: Niklas Wahlberg (LU), Sebastian Bromander (SLU), Johan DIxelius (SLU)
• Biosafety, import permits: Henrik Gradstedt (UU)
• Sampling and vouchering: Stefan Ekman (Uppsala Museum of Evolution)
• DNA extractions and sequencing: Olga Vinnere Pettersson (SciLifeLab Planetary Biology Capability)
• Bioinformatic pipelines, metadata and FAIR (SciLifeLab-NBIS)
• Swedish Reference Genome Portal: Daniel Brink (SciLifeLab Data Center)
• Data mobilization: Veronica Johansson (SBDI)

Program

9:00-9:30 Introduction: Current RefGen sequencing initiatives and what to consider before embarking on the RefGen generation trail, GoAT. Olga Vinnere Pettersson, SciLifeLab-Genomics / BGE

9:30 – 10:00 Sampling in the field and importance of vouchering. Stefan Ekman, UU Museum of Evolution

10:00 – 10:30 Coffee break

10:30 – 11:00 Nagoya Protocol and ABS requirements, CARE. Johan Dixelius, UU Unit for Research Support / Sebastian Bromander, SLU / Niklas Wahlberg, LU Museum

11:00 – 11:30 Sanitary/veterinary certification, import and export permits, CITES. SBA / Henrik Gradstedt, UU Unit for Biosecurity

11:30 – 12:00 Discussion and Q&A

12:00 – 13:00 Lunch

13:00 – 13:30 Shipment to sequencing facilities, sequencing facility requirements, tissue preservation for HMW-DNA and RNA extractions, as well as HiC protocols. Olga Vinnere Pettersson, SciLifeLab-Genomics / BGE

13:30 – 14:00 Nucleic acids extraction and sequencing, QC and protocols.io. Olga Vinnere Pettersson, SciLifeLab Genomics / BGE

14:00 – 14:30 Importance of metadata and FAIR, metadata collection format. SciLifeLab-NBIS / BGE

14:30 – 15:00 Coffee break

15:00 – 15:30 Data QC, Pipeline for Genome Assembly and Annotation. SciLifeLab-NBIS / BGE

15:30 – 16:00 Data deposition to open repositories. SciLifeLab-NBIS / BGE

16:00 – 16:30 Swedish Reference Genome Portal. Daniel Brink, SciLifeLab-Data Center

16:30 – 17:00 Data mobilization. Veronika Johansson, SBDI / GBIF

17:00 – 17:30 Discussions and Q&A

Other information

The course itself is free of charge. Coffee/tea and snacks as well as lunch will be provided during the course but participants are responsible for their own accommodations and travel

For questions, please contact olga.pettersson@igp.uu.se or anabella.aguilera@scilifelab.se