bacterial-genome-assembly/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Assembly of bacterial paired-end short read data
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input adapter trimmed sequence reads (forward) | #main/Input adapter trimmed sequence reads (forward) | Should be the adapter trimmed forward strand of the paired end reads. |
|
| Input adapter trimmed sequence reads (reverse) | #main/Input adapter trimmed sequence reads (reverse) | Should be the adapter trimmed reverse strand of the paired end reads. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | shovill_genome_assembly | genome assembly with shovill tool toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy2 |
| 3 | bandage_contig_graph_stats | bandage_contig_graph_stats toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2 |
| 4 | bandage_contig_graph_plot | bandage_contig_graph_plot toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 5 | ToolDistillator | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/1.0.0+galaxy1 |
| 6 | ToolDistillator summarize | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/1.0.0+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| bandage_contig_graph_plot | #main/bandage_contig_graph_plot | n/a |
|
| bandage_contig_graph_stats | #main/bandage_contig_graph_stats | n/a |
|
| shovill_alignment_bam | #main/shovill_alignment_bam | n/a |
|
| shovill_contigs_fasta | #main/shovill_contigs_fasta | n/a |
|
| shovill_contigs_graph | #main/shovill_contigs_graph | n/a |
|
| shovill_logfile | #main/shovill_logfile | n/a |
|
| tooldistillator_results_assembly | #main/tooldistillator_results_assembly | n/a |
|
| tooldistillator_summarize_assembly | #main/tooldistillator_summarize_assembly | n/a |
|
Version History
v1.0 (earliest) Created 18th Jun 2024 at 03:01 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.05c3e93f
Creators and Submitter
Tools
Activity
Views: 6475 Downloads: 2372 Runs: 4
Created: 18th Jun 2024 at 03:01
Last updated: 2nd Oct 2024 at 11:00
AttributionsNone
Related items
Advanced Spaces list for this Workflow with search and filtering
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/
Advanced Teams list for this Workflow with search and filtering
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
You can contribute too!
Space: Galaxy
Public web page: https://iwc.galaxyproject.org/
