RepeatExplorer Workshop 2014

Programme

Tuesday (May 27)

• 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 RepeatExplorer pipeline – new tools P. Novák
• 11:20 Using RepeatExplorer output for repeat annotation and quantification J. Macas
• 11:40 Extraction and phylogenetic analysis of transposon protein domains P. Neumann
• 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
  • analysis of retrotransposon protein domains

Wednesday (May 28)

• 9:00 – 12:00 Short talks (30 min each)
  • Gerhard Menzel (Dresden University of Technology, Germany) – The repetitive fraction of the saffron genome
  • Tony Heitkam (Dresden University of Technology, Germany) – Profiling repeats in Camellia japonica
  • Ana Moraes (Julio de Mesquita State University, Brazil) – The orchid chromosomes and genome size evolution: The beauty of Brazilian orchids is beyond its flowers!
  • Hans de Jong (Wageningen University, Netherlands) – Repeat distribution in tomato chromosome 7
  • André Marques (Federal University of Pernambuco, Brazil) – Identification of the first centromere-specific tandem repeat in a holocentric species
• 12:30 Lunch
• 13:30 – (18:00) Practical training II J. Macas, P. Novák, P. Neumann
  • structure of the output data from clustering analysis
  • repeat annotation and quantification
  • re-clustering
  • visualization and exploration of cluster graphs (SeqGrapheR)
  • design of probes from identified repetitive elements

Thursday (May 29)

• 9:00 – 12:30 Short talks
  • Yves Bigot, Peter Arensburger (Centre INRA Val de Loire, France) – Transposable elements in avian genomes
  • Martina Pavlek (Rudjer Boskovic Institute, Croatia) – Analysis of satellite DNAs in sequenced genome of Tribolium castaneum (Coleoptera)
  • Erica Ramos (São Paulo State University – UNESP, Brazil) – Integrative genomics analysis in the B chromosome of cichlid fish Astatotilapia latifasciata
  • Andrew Leitch, Lu Ma, Wencai Wang (Queen Mary University of London, UK) – Repeats in giant plant genomes
  • Hannes Becher (Queen Mary University of London, UK) – FriEPRV – a virus-derived centromeric element in crown imperial Fritillary (Fritillaria imperialis L.)
  • Steven Dodsworth (Queen Mary University of London, UK) –Repeat dynamics in closely related allopolyploid Nicotiana (Solanaceae)
• 12:30 Lunch
• 13:30 – (18:00) Practical training III – advanced topics and troubleshooting
  • running RepeatExplorer from a command line
  • clustering satellite DNA-rich genomes
  • comparative analysis of multiple genomes (study and analysis design, controls, evaluation of results, phylogenetic analysis of retroelements, etc.)
  • probe design based on k-mer analysis of satellite repeats