Open Galaxy server

RepeatExplorer

Most of a plant genome is repetitive

These tools identify repeats, classify them and estimate their abundance, either from low-coverage sequencing reads or from an assembled genome.

LTR retrotransposons Tandem repeats DNA transposons

The tools run on a public Galaxy server, on the command line, or as containers.

What each tool annotates

Working from sequencing reads

No assembly needed. Low-coverage shotgun reads are enough to find repeat families and estimate how much of the genome each one occupies.

  • RepeatExplorer2

    All Galaxy CLI

    Graph-based identification and quantification of repeats from unassembled sequencing reads

  • TAREAN

    Tandem Galaxy CLI

    Reconstructs satellite repeat consensus sequences from RepeatExplorer2 read clusters

  • ChIP-Seq Mapper

    Galaxy

    Compares ChIP and input read mapping across repeat clusters to find associated repeats

Working from a genome assembly

Annotate repeats along the assembled sequence, then merge the results into one non-overlapping annotation.

  • DANTE

    Domains Galaxy CLI

    Domain-based annotation of transposable elements using the REXdb protein database

  • DANTE_LTR

    LTR Galaxy CLI

    Identifies complete LTR retrotransposons from DANTE domain hits and classifies them into lineages

  • DANTE_TIR

    DNA Galaxy CLI

    Finds DNA transposons with terminal inverted repeats, seeded by transposase domains

  • TideCluster

    Tandem Galaxy CLI

    Detects tandem repeats in genome assemblies and clusters them into families

  • CARP

    LTR Tandem DNA Galaxy CLI

    Integrates the annotation tools into a single non-overlapping repeat annotation of a genome

Reference data

The protein domain database the annotation tools classify against.

  • REXdb

    Reference

    Reference database of transposable element protein domains, used for classification

Protocols

Step-by-step guides, from the published protocols for read-based work to the current workflow for annotating an assembly.

Workshops

Run most years since 2014. No workshop is currently announced — past programmes and slides are archived here.