Racon polish with long reads, x4

Assembly polishing subworkflow: Racon polishing with long reads

Inputs: long reads and assembly contigs

Workflow steps:

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
Racon long-read polished assembly => Fasta statistics
Note: The Racon tool panel can be a bit confusing and is under review for improvement. Presently it requires sequences (= long reads), overlaps (= the paf file created by minimap2), and target sequences (= the contigs to be polished) as per "usage" described here https://github.com/isovic/racon/blob/master/README.md
Note: Racon: the default setting for "output unpolished target sequences?" is No. This has been changed to Yes for all Racon steps in these polishing workflows. This means that even if no polishes are made in some contigs, they will be part of the output fasta file.
Note: the contigs output by Racon have new tags in their headers. For more on this see https://github.com/isovic/racon/issues/85.

Infrastructure_deployment_metadata: Galaxy Australia (Galaxy)

Inputs

ID	Name	Description	Type
Assembly to be polished	Assembly to be polished	n/a	File
long reads	long reads	n/a	File
minimap setting (for long reads)	minimap setting (for long reads)	n/a	string?

Steps

ID	Name	Description
3	Minimap2: map long reads to assembly	Map raw reads to assembly; output paf toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
4	Racon: polish 1	toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13
5	Minimap2: map long reads to polished assembly 1	Map raw reads to assembly; output paf toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
6	Racon: polish 2	toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13
7	Minimap2: map long reads to polished assembly 2	Map raw reads to assembly; output paf toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
8	Racon: polish 3	toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13
9	Minimap2: map long reads to polished assembly 3	Map raw reads to assembly; output paf toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.20+galaxy2
10	Racon: polish 4	toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.4.13

Outputs

ID	Name	Description	Type
Assembly polished by long reads using Racon	Assembly polished by long reads using Racon	n/a	File

Racon polish with long reads, x4
Version 1