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
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
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
Inputs
ID | Name | Description | Type |
---|---|---|---|
DRR187559_1 | #main/DRR187559_1 | forward read |
|
DRR187559_2 | #main/DRR187559_2 | reverse read |
|
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 |
|
DRR187559_filtered_1 | #main/DRR187559_filtered_1 | n/a |
|
Falco html_file (forward) | #main/Falco html_file (forward) | n/a |
|
Falco html_file (reverse) | #main/Falco html_file (reverse) | n/a |
|
Falco text_file (forward) | #main/Falco text_file (forward) | n/a |
|
Falco text_file (reverse) | #main/Falco text_file (reverse) | n/a |
|
bracken_kraken_report | #main/bracken_kraken_report | n/a |
|
bracken_report_tsv | #main/bracken_report_tsv | n/a |
|
fastp report_html | #main/fastp report_html | n/a |
|
fastp_json | #main/fastp_json | n/a |
|
kraken_report_reads | #main/kraken_report_reads | n/a |
|
kraken_report_tabular | #main/kraken_report_tabular | n/a |
|
recentrifuge_data_tabular | #main/recentrifuge_data_tabular | n/a |
|
recentrifuge_logfile | #main/recentrifuge_logfile | n/a |
|
recentrifuge_report_html | #main/recentrifuge_report_html | n/a |
|
recentrifuge_stats_tabular | #main/recentrifuge_stats_tabular | n/a |
|
Version History

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Views: 37 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 11:02


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