polish

polishing subworkflow

Polishing nanopore reads is the process of taking draft genomes and improving them through additional comparisons of the draft genomes with the relevant reads. Medaka uses nanopore reads to improve the draft genome. Polypolish and POLCA use Illumina reads. This workflow only uses one round of polish for each of these tools due to the increase in quality of nanopore reads. If there is a need for additional rounds of polishing, linking this workflow to another nextflow workflow is an option and instructions for doing so are covered in the linking workflows wiki page.

All draft genomes in their varying states of polishing are sent to busco in the metrics subworkflow for comparison.

Hybrid assembly does not use the polishing subworkflow.

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Donut Falls
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flowchart LR

A[assembled genome] --> B[medaka]
B --> C[polypolish]
C --> F[bwa]
F --> D[polca]
D --> E[consensus fasta]
G[illumina fastq] --> C
G --> F

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Relevant parameters (params) and their default values

params.medaka_options              = ''
params.polca_options               = ''
params.polypolish_options          = ''