Difference between revisions of "Ensembl Tools"

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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 21:20, 6 December 2019

Description

Ensembl_Tools website  

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

Required Modules

Serial

  • 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.



Citation

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

http://www.ensembl.org/info/about/publications.html


Validation

  • Validate 4/5/2018