Racon polish with long reads, x4
Version 1

Workflow Type: Galaxy

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 n/a
long reads long reads n/a n/a
minimap setting (for long reads) minimap setting (for long reads) n/a n/a
corrected_reads corrected_reads runtime parameter for tool Racon n/a
overlaps overlaps runtime parameter for tool Racon n/a
reads reads runtime parameter for tool Racon n/a

Steps

ID Name Description
0 Assembly to be polished
1 long reads
2 minimap setting (for long reads)
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
alignment_output alignment_output n/a
consensus consensus n/a
alignment_output alignment_output n/a
consensus consensus n/a
alignment_output alignment_output n/a
consensus consensus n/a
alignment_output alignment_output n/a
consensus consensus n/a

Version History

Version 1 (earliest) Created 8th Nov 2021 at 05:45 by Anna Syme

Added/updated 2 files


Open master 2ed2834
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Citation
Syme, A. (2021). Racon polish with long reads, x4. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.227.1
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Views: 1159   Downloads: 6

Created: 8th Nov 2021 at 05:45

Last updated: 9th Nov 2021 at 01:12

Last used: 2nd Dec 2022 at 06:37

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