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HELEN

Description

helen website

HELEN is a polisher intended to use for polishing human-genome assemblies. HELEN operates on the pileup summary generated by MarginPolish. MarginPolish uses a probabilistic graphical-model to encode read alignments through a draft assembly to find the maximum-likelihood consensus sequence. The graphical-model operates in run-length space, which helps to reduce errors in homopolymeric regions. MarginPolish can produce tensor-like summaries encapsulating the internal likelihood weights. The weights are assigned to each genomic position over multiple likely outcomes that is suitable for inference by a Deep Neural Network model.

Environment Modules

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

Environment Variables

  • HPC_HELEN_DIR - installation directory
  • HPC_HELEN_BIN - executable directory
  • HPC_HELEN_DAT - data directory

Categories

phylogenetics