Workflow Type: Galaxy
Open
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 |
|
Illumina reads, R1, in fastq.gz format | Illumina reads, R1, in fastq.gz format | n/a |
|
Steps
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 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Assembly polished by short reads using Racon | Assembly polished by short reads using Racon | n/a |
|
Version History
Version 1 (earliest) Created 8th Nov 2021 at 05:50 by Anna Syme
Added/updated 2 files
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master
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Creators and Submitter
Creator
Submitter
Citation
Syme, A. (2021). Racon polish with Illumina reads, x2. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.228.1
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Created: 8th Nov 2021 at 05:50
Last updated: 9th Nov 2021 at 01:09
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