RepeatExplorer Workshop 2016

Programme

Tuesday (May 24)

• 8:30 – 9:30 Registration
• 09:30 Principles of repeat identification in plant genomes and introduction to graph-based clustering J. Macas
• 10:10 RepeatExplorer pipeline – algorithms and implementation P. Novák
• 10:30 Coffee break
• 11:00 Using RepeatExplorer output for repeat annotation and quantification J. Macas
• 11:20 Transposon protein databases – recent updates to cover all Viridiplantae P. Neumann
• 11:40 New tools – ChIP-seq and satellite DNA analysis P. Novák
• 12:00 Lunch
• 13:30 – (18:00) Practical training I J. Macas, P. Novák, P. Neumann
  • introduction to Galaxy environment
  • overview of RepeatExplorer tools
  • pre-processing of NGS reads
  • setting up clustering analysis – single species
  • read pre-processing and clusterng analysis from the command line
  • comparative clustering of multiple samples

Wednesday (May 25)

• 9:00 – 12:00 Short presentations of workshop participants
  • Ilia Leitch (Royal Botanic Gardens, Kew, UK) – Genome diversity across land plants
  • Steven Dodsworth (Royal Botanic Gardens, Kew, UK) – Repeat dynamics in Nicotiana
  • Jamie McCann (University of Vienna, Austria) – Repeat dynamics in Melampodium
  • Tony Heitkam (TU Dresden, Germany) – Repeat analysis in the Camellia japonica genome
  • Anja Kögler (TU Dresden, Germany) – Exploring the origin of the Pillnitz Camellia (Camellia japonica)
  • Gerhard Menzel (TU Dresden, Germany) – Repetitive DNA families of the saffron crocus (Crocus sativus L.)
• 12:30 Lunch
• 13:30 – (18:00) Practical training II J. Macas, P. Novák, P. Neumann
  • identification and phylogenetic analysis of retrotransposon protein domains
  • cluster annotation and repeat composition of the genome
  • re-clustering and cluster merging
  • SeqGrapheR – visualization and annotation of the cluster graphs
  • comparative clustering of multiple species – data interpretation
  • repeat quantification (principles, sensitivity and reproducibility)

Thursday (May 26)

• 9:00 – 12:00 Short presentations of workshop participants
  • Aretuza Sousa dos Santos (University of Munich, Germany) – Genomic and in situ analyses of the repetitive DNA on the Y-chromosome of Coccinia grandis (Cucurbitaceae) in comparison to the X and autosomes
  • Nomar Waminal (Seoul National University, Korea) – A high-copy satellite DNA of Panax ginseng was derived from CACTA transposon and is a useful barcode for identifying individual chromosomes
  • Ilya Kirov (Institute for Agricultural and Fisheries Research, Melle, Belgium) – Towards a FISH-based karyotype of Rosa
  • Robin van Velzen (Wageningen University, Netherlands) – Expansion of Gypsy-type LTR retrotransposons in the nodulating non-legume Parasponia
  • Vratislav Peska (Masaryk University, Brno, Czech Republic) – BAL31-NGS identification of Allium telomeres
  • Iris Vargas Jentzsch (University of Cologne, Germany) – Repetitive trouble: the repetitive landscape of the milkweed bug Oncopeltus fasciatus
  • Hannes Becher (Queen Mary University of London, UK) – Transcribed repeats and Numts in a grasshopper with a giant genome
• 12:30 Lunch
• 13:30 – (18:00) Practical training III J. Macas, P. Novák, P. Neumann
  • design of hybridization probes based on RE output (dispersed repeats)
  • NEW TOOL: automated identification and characterization of satellite repeats (incl. probe design)
  • NEW TOOL: evaluation of ChIP-seq data
  • advanced topics, troubleshooting