Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available) 1.0
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Run on GalaxyGenome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
Associated Tutorial
This workflows is part of the tutorial Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bazante Sanders, Bérénice Batut
Tutorial Author(s): Bazante Sanders, Bérénice Batut
Tutorial Contributor(s): Helena Rasche, Bazante Sanders, Saskia Hiltemann, Miaomiao Zhou, Anthony Bretaudeau, Cristóbal Gallardo, Björn Grüning, Bérénice Batut, Matúš Kalaš
Funder(s): Avans Hogeschool, ABRomics
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Illumina forward raw reads | Illumina forward raw reads | Illumina forward raw reads |
|
| Illumina reverse raw reads | Illumina reverse raw reads | Illumina reverse raw reads |
|
| Nanopore raw reads | Nanopore raw reads | Nanopore raw reads |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Convert compressed file to uncompressed. | CONVERTER_bz2_to_uncompressed |
| 4 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 |
| 5 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
| 6 | NanoPlot | toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 |
| 7 | filtlong | toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.1+galaxy0 |
| 8 | Flye | toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 |
| 9 | NanoPlot | toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.41.0+galaxy0 |
| 10 | Bandage Image | toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 11 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 12 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 |
| 13 | BWA-MEM2 | toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1 |
| 14 | Polypolish | toolshed.g2.bx.psu.edu/repos/iuc/polypolish/polypolish/0.5.0+galaxy2 |
| 15 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| nanoplot_before_filtering | nanoplot_before_filtering | n/a |
|
| flye_assembly_info | flye_assembly_info | n/a |
|
| nanoplot_after_filtering | nanoplot_after_filtering | n/a |
|
| quast_report_before_polishing | quast_report_before_polishing | n/a |
|
| quast_report_after_polishing | quast_report_after_polishing | n/a |
|
Version History
master
Creators and Submitter
Views: 241 Downloads: 29 Runs: 1
Created: 2nd Jun 2025 at 11:01
AttributionsNone
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Organizations: Galaxy
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