Ensembl Tools

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Ensembl_Tools website  

Ensembl Tools provide a number of ready-made tools for processing sequence data.

Required Modules


  • Ensembl_Tools

Parallel (OpenMP)

  • intel
  • Ensembl_Tools

Parallel (MPI)

  • intel
  • openmpi
  • Ensembl_Tools

System Variables

  • HPC_ENSEMBL_TOOLS_DIR - installation directory

Additional Information

Available tools:

  • Variant Effect Predictor - analyse your own variants and predict the functional consequences of known and unknown variants via Ensembl Variant Effect Predictor (VEP) tool.
  • ID History converter - convert a set of Ensembl IDs from a previous release into their current equivalents.
  • Assembly converter - map (liftover) data's coordinates to the current assembly.
  • Region Reporter - A script for sampling a given set of chromosomalregions, producing a simple summary of the features within those regions. Operates in batch and single region mode, and can serialize into GFF3 and textual format.


If you publish research that uses Ensembl_Tools you have to cite it as follows:



  • Validate 4/5/2018