Checking expected species and contamination in bacterial isolate
Visit source
Download RO-CrateChecking 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
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Bérénice Batut
Tutorial Contributor(s): Clea Siguret
Workflow Author(s): Pierre, Bérénice Batut
Funder(s): ABRomics
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| forward_reads | #main/forward_reads | forward_reads |
|
| reverse_reads | #main/reverse_reads | reverse_reads |
|
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 |
|
| bracken_report_tsv | #main/bracken_report_tsv | 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
2.0 (latest) Created 16th Jul 2024 at 14:09 by Helena Rasche
Added/updated 4 files
Open
master15a562e
3.0 (earliest) Created 25th Jun 2024 at 11:11 by Helena Rasche
Added/updated 4 files
Frozen
3.0d7ec76d
Creators and Submitter
Views: 436 Downloads: 148
Created: 25th Jun 2024 at 11:11
Last updated: 25th Jun 2024 at 11:11
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
