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ONT assembly and Illumina polishing pipeline

https://github.com/nanoporetech/ont-assembly-polish

This pipeline performs the following steps:

  • Assembly of nanopore reads using Canu.
  • Polish canu contigs using racon (optional).
  • Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem.
  • Perform correction of contigs using pilon and the Illumina dataset.