PART I.  BASIC TRAINING (online, performed individually any time before May 23)

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 analyzing 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 23-25)

Tuesday (May 23)

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 Local installation and running RepeatExplorer2 from a command line

Wednesday (May 24)

8:30 – 12:00	Short presentations of workshop participants Ludwig Mann (Technische Universität Dresden, Germany) – The quest for consensus – from RepeatExplorer clusters to repeat scaffolds (a technical concept) Sophie Maiwald (Technische Universität Dresden, Germany) – Evolving together: 5S rRNA promoter mutations are mirrored in Cassandra retrotransposons Alexandr Sember (Institute of Animal Physiology and Genetics, Czech Rep.) – Glimpse into satellite DNA evolution in Nothobranchius annual killifishes coffee break James Walters (University of Kansas, USA) – Comparative analysis of sex-linked repeats in Danaine butterflies Vratislav Peška (Institute of Biophysics, Brno, Czech Republic) – Telomeres and telomerases Martin Lyčka (CEITEC & Faculty of Science, Masaryk University, Brno, Czech Rep.) – TeloBase: A community-curated database of telomere motifs across the tree of life
12:30	Lunch
13:30 – (18:00)	Practical training II – Genome annotation tools (J. Macas, P. Novák, P. Neumann) Tandem repeat annotation using TideCluster Designing FISH probes from TideCluster/TAREAN output REXdb, DANTE, and structure-based annotation of complete LTR-retrotransposons using DANTE_LTR
18:00 – 22:00	Conference dinner at restaurant Kampa

Thursday (May 25)

8:30 – 11:30	Short presentations of workshop participants Minoo Nasiri (Technische Universität Dresden, Germany) – Circular DNA in adverse conditions: a RepeatExplorer-based approach to investigate eccDNAs and TE activation Helena Štorchová (Institute of Experimental Botany, Praha, Czech Rep.) – De novo assembly of highly recombined plant mitochondrial genomes from Illumina short reads and ONT long reads – the example of Silene fabaria Valentin Hure (Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France) – Recruitment of Polycomb group proteins on transposable elements in Arabidopsis thaliana coffee break Johann Confais (URGI INRAE, France) – How to use REPET for de novo TE annotation
12:00	Lunch
13:30 – (18:00)	Practical training III REPET pipeline (Johann Confais, URGI INRAE, France) (+ topics proposed by the participants & individual consultations)