Protocols and guides

Guides for running the analyses, from the published protocols for read-based work to the current workflow for annotating a genome assembly.

• Genome annotation with DANTE_LTR and TideCluster on Galaxy

  Step-by-step annotation of LTR retrotransposons and tandem repeats in an assembly

• Published RepeatExplorer2 protocols

  The four protocols for read-based repeat analysis published in Nature Protocols

• Coverage and reproducibility

  How sequencing depth affects repeat abundance estimates, measured on pea

• RepeatExplorer manual (archived)

  The manual for the original Galaxy pipeline, kept as a historical record