ReapeatExplorer2 Manual and Protocols

Reproducibility of repeat identification

Presentations and training material from the 11th RepeatExplorer workshop (May 2023):

• Macas, J –  Principles and history of RepeatExplorer
• Neumann, P – Diagnostic features of repetitive elements
• Novak,P –  RepeatExplorer tools for genome annotation
• VirtualBox image used for training:  https://t.ly/r_eO
• Command line practicals:  https://github.com/repeatexplorer/workshop
• TideCluster manual: https://github.com/kavonrtep/TideCluster
• Workshop manual: pdf

Presentations from the 10th RepeatExplorer workshop (May 2022):

• Macas, J – RepeatExplorer – history and principles
• Neumann, P – Diagnostic features of repetitive elements
• Novak, P – Assembly annotation tools

Presentations from the 9th RepeatExplorer workshop (May/June 2021):

• Novak, P. – RepeatExplorer pipeline and associated tools
• Macas, J. – RepeatExplorer applications
• Neumann, P. – REXdb database and DANTE
• Macas, J. – Using RE output for repeat annotation and quantification

Video tutorials for practical training during the 9th RepeatExplorer workshop

• Galaxy environment and RepeatExplorer server (P. Novak)
• Protocol 1: Repeat analysis in a single species (J. Macas)
• Protocol 2: Comparative repeat analysis in multiple species (J. Macas)
• Structure of the RepeatExplorer output files (P. Novak)
• Protocols 1 + 2: evaluation and interpretation of the results, downstream analysis, data visualization tools  (J. Macas)
• Protocol 3: TAREAN analysis of satDNA and FISH probe design (P. Neumann)
• Protocol 4: Identification of centromeric repeats using ChIP-seq analysis (P. Neumann)
• DANTE and JBrowse (P. Novak)