Quality and contamination control in bacterial isolate using Illumina MiSeq Data 2.0
Visit source
Download RO-Crate
Run on GalaxyQuality 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
master
Creators and Submitter
Views: 1160 Downloads: 163 Runs: 0
Created: 2nd Jun 2025 at 11:02
Tags AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
