Medaka

MedakaPolish

description
Polish an ONT draft assembly with GUPPY basecalled ONT reads. Runs within a few hours with 18GB basecalled_reads and a 23Mb genome

Inputs

Required

  • basecalled_reads (File, required): basecalled reads to be used with polishing
  • draft_assembly (File, required): draft assembly to be polished

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • model (String, default="r941_prom_high_g360"): run medaka tools list_models and pick string with the correct pore type, machine, and guppy version
  • n_rounds (Int, default=3): number of polishing rounds to apply
  • prefix (String, default="consensus"): prefix for output files
  • zones (String, default="us-central1-a us-central1-b us-central1-c us-central1-f")

Outputs

  • polished_assembly (File)