Workflow Type: Galaxy
Open
Genome 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 using Oxford Nanopore MinION (and Illumina data if available), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Bazante Sanders, Bérénice Batut
Tutorial Contributor(s): Helena Rasche, Bazante Sanders, Saskia Hiltemann, Miaomiao Zhou
Workflow Author(s): Bazante Sanders, Bérénice Batut
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
1.0 (earliest) Created 25th Jun 2024 at 11:06 by Helena Rasche
Added/updated 4 files
Open
master
48d6b32
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Activity
Views: 448 Downloads: 119
Created: 25th Jun 2024 at 11:06
Last updated: 25th Jun 2024 at 11:06
Attributions
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