Ensembl Tools¶
Description¶
Ensembl Tools provide a number of ready-made tools for processing sequence data.
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 chromosomal regions, 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.
Environment Modules¶
Run module spider ensembl_tools to find out what environment modules are available for this application.
Environment Variables¶
- HPC_ENSEMBL_TOOLS_DIR - installation directory
Additional Usage 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.
Required Modules¶
Serial
- Ensembl_Tools
Parallel (OpenMP)
- Intel
- Ensembl_Tools
Parallel (MPI)
- Intel
- Open MPI
- Ensembl_Tools
Citation¶
If you publish research that uses Ensembl Tools, you have to cite it as follows:
Categories¶
biology