Racon polish with Illumina reads, x2
Version 1

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)

Inputs

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

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

Version History

Version 1 (earliest) Created 8th Nov 2021 at 05:50 by Anna Syme

Added/updated 2 files


Open master c0f4401
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Citation
Syme, A. (2021). Racon polish with Illumina reads, x2. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.228.1
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Views: 686   Downloads: 3

Created: 8th Nov 2021 at 05:50

Last updated: 9th Nov 2021 at 01:09

Last used: 12th Aug 2022 at 03:05

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