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marginpolish website  

MarginPolish is a graph-based assembly polisher. It iteratively finds multiple probable alignment paths for run-length-encoded reads and uses these to generate a refined sequence. It takes as input a FASTA assembly and an indexed BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly.

While MarginPolish serves as a standalone assembly polisher, it is also part of an assembly pipeline which includes an ultrafast nanopore assembler Shasta and a multi-task RNN polisher HELEN. HELEN operates on images generated by MarginPolish.

Environment Modules

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

System Variables

  • HPC_MARGINPOLISH_DIR - installation directory
  • HPC_MARGINPOLISH_BIN - executable directory