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uropa

Description

uropa website

UROPA (‘Universal RObust Peak Annotator’) is a command line based tool, intended for universal genomic range (e.g. peaks) annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (eg. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources, as well as custom reference annotation files produced by the user. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R.

Environment Modules

Run module spider uropa to find out what environment modules are available for this application.

Environment Variables

  • HPC_UROPA_DIR - installation directory
  • HPC_UROPA_BIN - executable directory

Citation

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

Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports 7 (2017), doi: 10.1038/s41598-017-02464-y

Categories

genomics, sequencing, biology