Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)
1.0

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Workflow Type: Galaxy

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

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1178?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

1.0 (earliest) Created 25th Jun 2024 at 11:06 by Helena Rasche

Added/updated 4 files


Open master 48d6b32
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
fastp
NanoPlot
Filtlong
Flye
Bandage
Bwa-mem2
QUAST
Polypolish
License
MIT License
Activity

Views: 447   Downloads: 119

Created: 25th Jun 2024 at 11:06

Last updated: 25th Jun 2024 at 11:06

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Total size: 177 KB
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