RepeatExplorer Workshop 2023

Programme

Tuesday (May 23)

• 8:00 – 9:00 Registration
• 09:00 Principles and history of RepeatExplorer J. Macas
• 10:00 Diagnostic features of repetitive elements – Part I P. Neumann
• 10:30 Coffee break
• 11:00 Diagnostic features of repetitive elements – Part II P. Neumann
• 11:15 RepeatExplorer tools for genome annotation P. Novák
• 12:30 Lunch
• 13:30 – (18:00) Practical training I J. Macas, P. Novák, P. Neumann
  • Basic Protocols 1-4: troubleshooting & advanced data analysis
  • Local installation and running RepeatExplorer2 from a command line

Wednesday (May 24)

• 8:30 – 12:00 Short presentations of workshop participants
  • Ludwig Mann (Technische Universität Dresden, Germany) – The quest for consensus – from RepeatExplorer clusters to repeat scaffolds (a technical concept)
  • Sophie Maiwald (Technische Universität Dresden, Germany) – Evolving together: 5S rRNA promoter mutations are mirrored in Cassandra retrotransposons
  • Alexandr Sember (Institute of Animal Physiology and Genetics, Czech Rep.) – Glimpse into satellite DNA evolution in Nothobranchius annual killifishes
  • coffee break
  • James Walters (University of Kansas, USA) – Comparative analysis of sex-linked repeats in Danaine butterflies
  • Vratislav Peška (Institute of Biophysics, Brno, Czech Republic) – Telomeres and telomerases
  • Martin Lyčka (CEITEC & Faculty of Science, Masaryk University, Brno, Czech Rep.) – TeloBase: A community-curated database of telomere motifs across the tree of life
• 12:30 Lunch
• 13:30 – (18:00) Practical training II – Genome annotation tools J. Macas, P. Novák, P. Neumann
  • Tandem repeat annotation using TideCluster
  • Designing FISH probes from TideCluster/TAREAN output
  • REXdb, DANTE, and structure-based annotation of complete LTR-retrotransposons using DANTE_LTR
• 18:00 – 22:00 Conference dinner at restaurant Kampa

Thursday (May 25)

• 8:30 – 11:30 Short presentations of workshop participants
  • Minoo Nasiri (Technische Universität Dresden, Germany) – Circular DNA in adverse conditions: a RepeatExplorer-based approach to investigate eccDNAs and TE activation
  • Helena Štorchová (Institute of Experimental Botany, Praha, Czech Rep.) – De novo assembly of highly recombined plant mitochondrial genomes from Illumina short reads and ONT long reads – the example of Silene fabaria
  • Valentin Hure (Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France) – Recruitment of Polycomb group proteins on transposable elements in Arabidopsis thaliana
  • coffee break
  • Johann Confais (URGI INRAE, France) – How to use REPET for de novo TE annotation
• 12:00 Lunch
• 13:30 – (18:00) Practical training III
  • REPET pipeline (Johann Confais, URGI INRAE, France)
  • (+ topics proposed by the participants & individual consultations)