Preliminary programme

Tuesday (May 21)

8:30 – 9:30 Registration
09:30 Principles and applications of graph-based repeat clustering (J. Macas)
10:10 RepeatExplorer pipeline  (P. Novák)
10:30 Coffee break
11:00 Using RepeatExplorer output for repeat annotation and quantification (J. Macas)
11:20 REXdb database and transposon classification using conserved protein domains (P. Neumann)
11:40 Additional tools – assembly annotation, ChIP-seq, processing OxfordNanopore reads, etc.  (P. Novák)
12:00 Lunch
14:00 – (18:00) Practical training I (J. Macas, P. Novák, P. Neumann)

  • design of sequencing and repeat analysis experiments
  • introduction to Galaxy environment
  • quality control and pre-processing of NGS reads, dealing with various read formats
  • setting up clustering analysis
  • comparative clustering of multiple samples

Wednesday (May 22)

9:00 – 12:00 Short presentations of workshop participants

12:30 Lunch
13:30 – (18:00) Practical training II

  • identification of satellite DNA using TAREAN
  • understanding RepeatExplorer output
  • cluster annotation and repeat composition of the genome
  • comparative clustering of multiple species – data interpretation
  • repeat quantification (principles, sensitivity and reproducibility)
  • design of hybridization probes based on RE output

Thursday (May 23)

9:00 – 12:30 Short presentations of workshop participants

12:30 Lunch
13:30 – (18:00) Practical training III

  • combining repeat clustering with ChIP-seq data
  • identification and phylogenetic analysis of retrotransposon protein domains
  • Assembly annotation
  • advanced topics, troubleshooting