Quality and contamination control in bacterial isolate using Illumina MiSeq Data 1.0
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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, Tristan Reynolds
Tutorial Author(s): Bérénice Batut, Clea Siguret
Tutorial Contributor(s): Verena Moosmann, Tristan Reynolds, Björn Grüning, Saskia Hiltemann, Teresa Müller, Bérénice Batut, Clea Siguret, Wolfgang Maier
Funder(s): ABRomics, The University of Melbourne, Melbourne Bioinformatics, Australian BioCommons
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input Paired Reads | #main/Input Paired Reads | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Falco | toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0 |
| 2 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy3 |
| 3 | Kraken2 | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy2 |
| 4 | Bracken | toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/3.1+galaxy0 |
| 5 | Recentrifuge | toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.16.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Falco html_file (forward) | #main/Falco html_file (forward) | n/a |
|
| Falco text_file (forward) | #main/Falco text_file (forward) | 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_report_html | #main/recentrifuge_report_html | n/a |
|
| recentrifuge_stats_tabular | #main/recentrifuge_stats_tabular | n/a |
|
Version History
master
Creators and Submitter
Views: 739 Downloads: 109 Runs: 1
Created: 22nd Dec 2025 at 13:14
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Organizations: Galaxy
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