PART I.  BASIC TRAINING (online, performed individually any time before May 24)

It is strongly recommended that all inexperienced RepeatExplorer users go through the tutorials listed below and perform all the hands-on tasks associated with them. The tutorials cover everything from setting up the user account on a public RepeatExplorer server, preparing input sequence data, and running four basic protocols that demonstrate various uses of RE, to downloading the data and then analysing it. These topics are not covered in the hands-on training sessions of the workshop, with the exception of using some of their output data for specific training and troubleshooting.

Online tutorials:

• Galaxy environment and RepeatExplorer server [VIDEO tutorial]
• Protocol 1: Repeat analysis in a single species [VIDEO tutorial]
• Protocol 2: Comparative repeat analysis in multiple species [VIDEO tutorial]
• Structure of the RepeatExplorer output files [VIDEO tutorial]
• Protocols 1 + 2: evaluation and interpretation of the results, downstream analysis, data visualization tools [VIDEO tutorial]
• Protocol 3: TAREAN analysis of satDNA and FISH probe design [VIDEO tutorial]
• Protocol 4: Identification of centromeric repeats using ChIP-seq analysis [VIDEO tutorial]

Please see the information below each video tutorial for links to additional resources. The protocols are also fully described in the publication:
Novak, P., Neumann, P., Macas, J. (2020) – Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nature Protocols 15:3745–3776.

PART II.  WORKSHOP (in person, May 24-26)

Tuesday (May 24)

8:00 – 9:00	Registration
09:00	Principles and history of RepeatExplorer (J. Macas)
10:00	Diagnostic features of repetitive elements – Part I  (P. Neumann)
10:30	Coffee break
11:00	Diagnostic features of repetitive elements – Part II  (P. Neumann)
11:15	RepeatExplorer tools for genome annotation (P. Novák)
12:30	Lunch
13:30 – (18:00)	Practical training I (J. Macas, P. Novák, P. Neumann) Basic Protocols 1-4: troubleshooting & advanced data analysis
19:00 – 22:00	Dinner at CITYgastro restaurant

Wednesday (May 25)

8:30 – 12:30	Short presentations of workshop participants Nicola Schmidt (Technische Universität Dresden, Germany) – The fancy ones are spotted first: an update on repeats in beets Ludwig Mann (Technische Universität Dresden, Germany) – Comparative repeat analysis of saffron (Crocus sativus) and its progenitor species Zirlane Portugal da Costa (University of Sao Paulo, Brazil) – The repetitive portion of Passifloraceae genomes coffee break Pol Fernández Mató (Institut Botànic de Barcelona, Spain) – Understanding genus wide genome size differences in Phoradendron Yennifer Mata-Sucre (Federal University of Pernambuco, Brazil) – Insight into the evolution of the repetitive fraction of the monocentric genus Juncus Nusrat Sultana (Technische Universität Dresden, Germany) – Development of molecular cytogenetics tools for the characterization of mango (Mangifera indica)
12:30	Lunch
13:30 – (18:00)	Practical training II – Genome annotation tools using RE output for annotating genome assemblies REXdb and DANTE structure-based annotation of complete LTR-retrotransposons

Thursday (May 26)

8:30 – 12:30	Short presentations of workshop participants Matej Lexa (Masaryk University, Brno, Czech Republic) – TE-greedy-nester: a tool to detect nested LTR-TEs in assembled genomes Monika Čechová  (Masaryk University, Brno, Czech Republic) – HiC-TE: a Nextflow pipeline to study repeat interactions in the 3D genome Sophie Maiwald (Technische Universität Dresden, Germany) – Hidden repeats: identifying non-autonomous LTR retrotransposons Vratislav Peška (Institute of Biophysics, Brno, Czech Republic) – New telomeres and telomerases coffee break Camila do Nascimento Moreira (Universidade Estadual Paulista, Brazil) – Comparative analysis of repetitive content in genomes of a rodent and a fish species with and without B chromosomes Veit Herklotz (Senckenberg Museum of Natural History Görlitz, Germany) – Repeatomic fingerprint – a statistical approach to track phylogenetic signals from comparative cluster analysis Alice Krumpolcová (Institute of Biophysics, Brno, Czech Republic) – Reconstruction of phylogenies in liverworts (Marchantiophyta) using a repeatome fingerprint
12:30	Lunch
13:30 – (18:00)	Practical training III – Advanced topics reconstructing phylogenetic relationships based on repeat sequence similarities (Steven Dodsworth, University of Portsmouth, UK) local installation and running RE tools from a command line topics proposed by the participants & individual consultations