Checking expected species and contamination in bacterial isolate
2.0

Workflow Type: Galaxy

Checking expected species and contamination in bacterial isolate

Associated Tutorial

This workflows is part of the tutorial Checking expected species and contamination in bacterial isolate, available in the GTN

Features

Thanks to...

Workflow Author(s): Pierre, Bérénice Batut

Tutorial Author(s): Bérénice Batut

Tutorial Contributor(s): Clea Siguret, Helena Rasche, Saskia Hiltemann

Funder(s): ABRomics

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
forward_reads #main/forward_reads forward_reads
  • File
reverse_reads #main/reverse_reads reverse_reads
  • File

Steps

ID Name Description
2 Kraken2 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1
3 Bracken toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0
4 Recentrifuge toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0

Outputs

ID Name Description Type
bracken_kraken_report #main/bracken_kraken_report n/a
  • File
bracken_report_tsv #main/bracken_report_tsv 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 11:03 by GTN Bot

Added/updated 4 files


Open master d10976d
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Views: 38   Downloads: 3   Runs: 0

Created: 2nd Jun 2025 at 11:03

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