RepeatExplorer Workshop 2018

Dates: 22-24 May 2018
Lecturers: Jiří Macas, Petr Novák, Pavel Neumann, N. Hoštáková

Programme

Tuesday (May 22)

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 Transposon protein databases P. Neumann
11:40 Assembly annotation using Profrep and DANTE N. Hoštáková
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 23)

9:00 – 12:00
Short presentations of workshop participants
- Lucia Campos-Dominguez (Royal Botanical Garden Edinburgh, UK) – Using Repeat Explorer to find the genomic factors driving speciation in Begonia
- Steven Dodsworth (University of Bedfordshire, UK) – Repeat dynamics in the largest diploid angiosperms, Fritillaria (Liliaceae)
- Floris C. Breman (Wageningen University, Netherlands) – The Pelargonium repeatome as a ‘DNA barcode’
- Hanna Schneeweiss (University of Vienna, Austria) – Repeat dynamics in wild and cultivated chile peppers (genus Capsicum)
- Daniel Vitales (Institut Botànic de Barcelona, Spain) – Transposon dynamics and chromosome reorganizations drive genome size evolution in Anacyclus
- Veit Herklotz (Senckenberg Museum for Natural History Görlitz, Germany) – Characterization of CANR4 satellite repeat in roses
- Danijela Greguraš (Institute of Botany, Pruhonice, Czech Republic) – Characterization of satellite and centromeric repeats in genus Hieracium
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 24)

9:00 – 12:30
Short presentations of workshop participants
- Andrew Leitch (Queen Mary University of London, UK) – The phylogenetic placement of Gnetales is important to understand patterns of genome evolution across seed plants: insights from Gnetum montanum genome
- Sonia Garcia (Institut Botànic de Barcelona, Spain) – Ribosomal DNA arrangements in Asteraceae: variability of 5S and 35S examined with TAREAN and RepeatExplorer
- Aleš Kovařík (Institute of Biophysics, Brno, Czech Republic) – Diversity of rDNA repeats in gymnosperms analysed by Repeat Explorer and other tools
- Vratislav Peška (Institute of Biophysics, Brno, Czech Republic) – Telomeres – current challenges
- Diogo C. Cabral-de-Mello (UNESP-Universidade Estadual Paulista, Brazil) – Satellite DNAs and sex chromosomes evolution in Orthoptera
- Nils Pilotte (Smith College, Northampton, USA) – Tropical parasites: improved diagnostics utilizing repetitive targets
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