Racon polish with Illumina reads, x2
Version 1

Run on Galaxy

Workflow Type: Galaxy

Assembly polishing subworkflow: Racon polishing with short reads

Inputs: short reads and assembly (usually pre-polished with other tools first, e.g. Racon + long reads; Medaka)

Workflow steps:

minimap2: short reads (R1 only) are mapped to the assembly => overlaps.paf. Minimap2 setting is for short reads.
overlaps + short reads + assembly => Racon => polished assembly 1
using polished assembly 1 as input; repeat minimap2 + racon => polished assembly 2
Racon short-read polished assembly => Fasta statistics

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

SEEK ID: https://workflowhub.eu/workflows/228?version=1

DOI: 10.48546/workflowhub.workflow.228.1

Inputs

ID	Name	Description	Type
Assembly to be polished	Assembly to be polished	n/a	File
Illumina reads, R1, in fastq.gz format	Illumina reads, R1, in fastq.gz format	n/a	File

ID	Name	Description
2	Minimap2 round 1: map reads to assembly	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
3	Racon round 1: polish assembly	toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13
4	Minimap2 round 2: map reads to assembly	toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
5	Racon round 2: polish assembly	toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13