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Assembly Polishing

subworkflows/local/polish_assemblies

Steps

  1. Final polishing proceeds differently depending on whether the sample is Illumina or Pacbio.

  2. Illumina A custom script is implemented to iteratively polish assemblies with reads based on a set number of iterations (DEFAULT 3).

    • Polishing uses Pilon and minimap2, with reads being mapped back to the polished assembly each time.
  3. Nanopore Medaka consensus is used to polish reads, a model must be specified by the user for polishing.
  4. Pacbio No addtional polishing is performed, outputs of Pacbio data still need to be tested.

Input

  • cleaned reads (fastq) from the FinalReads dir
  • This is the final reads file from the last step in the Clean Reads workflow (taking into account any skip flags that have been used)
  • Contig file (fasta) from the FinalAssembly dir
  • This is the final contig file from the last step in the CleanAssemble workflow (taking into account any skip flags that have been used)

Outputs

  • Assembly
  • Assembling
    • ConsensusGeneration
      • Polishing
        • Pilon
          • BAMs
          • Changes
          • Fasta
          • VCF
        • Racon
          • Consensus