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 RepeatExplorer2Nature 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
19:00 – 22:00 Conference dinner

Wednesday (May 24)

8:30 – 12:30 Short presentations of workshop participants

  • TBA
12:30 Lunch
13:30 – (18:00) Practical training II – Genome annotation tools

  • REPET pipeline (presented by Johann Confais, INRAE, France)

Thursday (May 25)

8:30 – 12:30 Short presentations of workshop participants

  • TBA
12:30 Lunch
13:30 – (18:00) Practical training III – Advanced topics

  • local installation and running RE tools from a command line
  • topics proposed by the participants & individual consultations