RepeatExplorer Workshop 2015

Programme

Tuesday (May 26)

• 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
• Towards automated classification of repeats: introducing a new version of RepeatExplorer
• 11:00 Using RepeatExplorer output for repeat annotation and quantification J. Macas
• 11:20 Transposon protein databases P. Neumann
• 11:40 Implementation of automated repeat annotation 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 27)

• 9:00 – 12:00 Short talks (20 min each)
  • Sarah Gomes de Oliveira (Queen Mary University of London, UK) – Repetitive sequences, chromosomes and evolution of Saccharum spp.
  • Tomas Fer (Charles University, Prague, Czech Rep.) – Repetitive sequences in the ginger family (Zingiberaceae)
  • Bruna Piereck (Universidade Federal de Pernambuci, Brasil) – Identification and Characterization of Transposable elements (Class II) in Glycine max and Vigna unguiculata
  • Wencai Wang (Queen Mary University of London, UK) – Intragenomic ribosomal DNA diversity in gymnosperms
  • coffee break
  • Vratislav Peška (Inst. Biophysics, Brno, Czech Rep.) – New telomeric motif in plant Cestrum (Solanaceae) identified in RepeatExplorer
  • Jana Dluhošová (Masaryk University, Brno, Czech Rep.) – Repetitive elements in zigzag clover (Trifolium medium L.)
  • Aretuza Sousa dos Santos (University of Munich, Germany) – Using RepeatExplorer to study the huge Y chromosome of Coccinia grandis (Cucurbitaceae)
• 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 28)

• 9:00 – 12:30 Short talks (20 min each)
  • Hanna Schneeweiss (University of Vienna, Austria) – Evolution of repeats in allopolyploids of Melampodium
  • Teresa Kowar (TU Dresden, Germany) – CenH3 and H3K9me2 associated sequences in sugar beet (Beta vulgaris)
  • Yung-I Lee (National Museum of Natural Science, Taiwan) – Localization of satellite repeats in Paphiopediulm species
  • coffee break
  • Hannes Becher (Queen Mary University of London, UK) – Specific repeats on neo-sex chromosomes – an example of RE use (plus pairshow – the secret mating life of paired reads)
  • Sebastián Pita (Facultad de Ciencias, Universidad de la República, Uruguay) – Transposable elements in Triatominae (Insecta: Hemiptera)
  • Ricardo Utsunomia (São Paulo State University, Brasil) – Cytogenetic and molecular analyses in the B chromosomes of the fish species Moenkhausia sanctaefilomenae
  • Duílio Silva (UNESP, Brasil) – Functional and evolutionary analysis of the B chromosome of Astyanax paranae (Characiformes, Characidae)
• 12:30 Lunch
• 13:30 – (18:00) Practical training III J. Macas, P. Novák, P. Neumann
  • design of hybridization probes based on RE output
  • advanced topics (filtering of satellite repeat reads before clustering; detection of telomeric and other simple repeats in NGS reads, k-mer analysis of satellite repeats)
  • troubleshooting