Quality and contamination control in bacterial isolate using Illumina MiSeq Data
2.0

Workflow Type: Galaxy

Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Associated Tutorial

This workflows is part of the tutorial Quality and contamination control in bacterial isolate using Illumina MiSeq Data, available in the GTN

Features

Thanks to...

Workflow Author(s): Bérénice Batut, Clea Siguret

Tutorial Author(s): Bérénice Batut, Clea Siguret

Tutorial Contributor(s): Verena Moosmann, Björn Grüning, Saskia Hiltemann, Teresa Müller, Bérénice Batut, Clea Siguret, Wolfgang Maier

Funder(s): ABRomics

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
DRR187559_1 #main/DRR187559_1 forward read
  • File
DRR187559_2 #main/DRR187559_2 reverse read
  • File

Steps

ID Name Description
2 Falco toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0
3 Falco toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0
4 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
5 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
6 Bracken toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0
7 Recentrifuge toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0

Outputs

ID Name Description Type
DRR187559_filtered_ #main/DRR187559_filtered_ n/a
  • File
DRR187559_filtered_1 #main/DRR187559_filtered_1 n/a
  • File
Falco html_file (forward) #main/Falco html_file (forward) n/a
  • File
Falco html_file (reverse) #main/Falco html_file (reverse) n/a
  • File
Falco text_file (forward) #main/Falco text_file (forward) n/a
  • File
Falco text_file (reverse) #main/Falco text_file (reverse) n/a
  • File
bracken_kraken_report #main/bracken_kraken_report n/a
  • File
bracken_report_tsv #main/bracken_report_tsv n/a
  • File
fastp report_html #main/fastp report_html n/a
  • File
fastp_json #main/fastp_json n/a
  • File
kraken_report_reads #main/kraken_report_reads n/a
  • File
kraken_report_tabular #main/kraken_report_tabular n/a
  • File
recentrifuge_data_tabular #main/recentrifuge_data_tabular n/a
  • File
recentrifuge_logfile #main/recentrifuge_logfile n/a
  • File
recentrifuge_report_html #main/recentrifuge_report_html n/a
  • File
recentrifuge_stats_tabular #main/recentrifuge_stats_tabular n/a
  • File

Version History

2.0 (earliest) Created 2nd Jun 2025 at 11:02 by GTN Bot

Added/updated 4 files


Open master 461c4b5
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Created: 2nd Jun 2025 at 11:02

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