Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/999?version=1

Inputs

ID Name Description Type
Illumina forward raw reads Illumina forward raw reads Illumina forward raw reads
  • File
Illumina reverse raw reads Illumina reverse raw reads Illumina reverse raw reads
  • File
Nanopore raw reads Nanopore raw reads Nanopore raw reads
  • File

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
  • File
flye_assembly_info flye_assembly_info n/a
  • File
nanoplot_after_filtering nanoplot_after_filtering n/a
  • File
quast_report_before_polishing quast_report_before_polishing n/a
  • File
quast_report_after_polishing quast_report_after_polishing n/a
  • File

Version History

1 (earliest) Created 22nd Apr 2024 at 11:17 by Helena Rasche

Added/updated 3 files


Open master 4e336f3
help Creators and Submitter
Creators
  • Bazante Sanders
  • Bérénice Batut
Submitter
Tools
FastQC
fastp
NanoPlot
Filtlong
Flye
Bandage
Bwa-mem2
QUAST
Polypolish
License
MIT License
Activity

Views: 31

Created: 22nd Apr 2024 at 11:17

Last updated: 22nd Apr 2024 at 11:17

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Total size: 40.5 KB
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