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Assembly polishing with long reads

Racon polish with long reads, x4

  • Author(s):
  • Anna Syme
  • Release: 0.1
  • License: MIT
  • UniqueID: 68d6270a-bfd1-452a-abc9-4a314e13af85

Assembly polishing with Racon workflow

Inputs

  • Sequencing reads in format: fastq, fastq.gz, fastqsanger.gz or fastqsanger
  • Genome assembly to be polished, in fasta format

What does the workflow do

  • After long reads have been assembled into a genome (contigs), this can be polished with the same long reads.
  • This workflow uses the tool minimap2 to map the long reads back to the assembly, and then uses Racon to make polishes.
  • This is repeated a further 3 times.

In more detail:

  • minimap2 : long reads are mapped to assembly => overlaps.paf.
  • overaps, long reads, assembly => Racon => polished assembly 1
  • using polished assembly 1 as input; repeat minimap2 + racon => polished assembly 2
  • using polished assembly 2 as input, repeat minimap2 + racon => polished assembly 3
  • using polished assembly 3 as input, repeat minimap2 + racon => polished assembly 4

Settings

  • Run as-is or change parameters at runtime.
  • For the input at "minimap settings for long reads", enter (map-pb) for PacBio reads, (map-hifi) for PacBio HiFi reads, or (map-ont) for Oxford Nanopore reads.

Outputs

There is one output: the polished assembly in fasta format.