bacterial-genome-assembly/main
View on GitHub
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Frozen
Frozen
Tests Assembly of bacterial paired-end short read data with generation of quality metrics and reports
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 | quast_quality | quast_quality toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1 |
| 4 | refseqmasher_genome | refseqmasher_genome, search close reference genome in refseq database toolshed.g2.bx.psu.edu/repos/nml/refseq_masher/refseq_masher_matches/0.1.2 |
| 5 | bandage_contig_graph_stats | bandage_contig_graph_stats toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2 |
| 6 | bandage_contig_graph_plot | bandage_contig_graph_plot toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 7 | ToolDistillator | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy1 |
| 8 | ToolDistillator summarize | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.1+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 |
|
| quast_log | #main/quast_log | n/a |
|
| quast_report_html | #main/quast_report_html | n/a |
|
| quast_report_pdf | #main/quast_report_pdf | n/a |
|
| quast_report_tabular | #main/quast_report_tabular | n/a |
|
| refseqmasher_report_tabular | #main/refseqmasher_report_tabular | 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 | #main/tooldistillator_results | n/a |
|
| tooldistillator_summarize | #main/tooldistillator_summarize | n/a |
|
Version History
v1.1.4 (latest) Created 26th Oct 2024 at 03:02 by WorkflowHub Bot
Updated to v1.1.4
Frozen
v1.1.4b8cdba4
v1.0 (earliest) Created 18th Jun 2024 at 03:01 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
5c3e93f
Creators and Submitter
Tools
Activity
Views: 1901 Downloads: 500 Runs: 0
Created: 18th Jun 2024 at 03:01
Last updated: 2nd Oct 2024 at 11:00
AttributionsNone
Related items
Advanced Teams list for this Workflow with search and filtering
IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
