bacterial-genome-assembly/main
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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/5.3.0+galaxy0 |
| 4 | checkm2_quality | Checkm2 to predict the completeness and contamination in an assembly toolshed.g2.bx.psu.edu/repos/iuc/checkm2/checkm2/1.0.2+galaxy1 |
| 5 | 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 |
| 6 | bandage_contig_graph_stats | bandage_contig_graph_stats toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/2022.09+galaxy2 |
| 7 | bandage_contig_graph_plot | bandage_contig_graph_plot toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 |
| 8 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 9 | ToolDistillator | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.2+galaxy0 |
| 10 | ToolDistillator summarize | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.9.2+galaxy0 |
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 |
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| checkm2_diamond_files | #main/checkm2_diamond_files | n/a |
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| checkm2_protein_files | #main/checkm2_protein_files | n/a |
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| checkm2_quality_report | #main/checkm2_quality_report | n/a |
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| quast_log | #main/quast_log | n/a |
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| quast_report_html | #main/quast_report_html | n/a |
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| quast_report_pdf | #main/quast_report_pdf | n/a |
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| quast_report_tabular | #main/quast_report_tabular | n/a |
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| refseqmasher_report_tabular | #main/refseqmasher_report_tabular | n/a |
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| shovill_alignment_bam | #main/shovill_alignment_bam | n/a |
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| shovill_contigs_fasta | #main/shovill_contigs_fasta | n/a |
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| shovill_contigs_graph | #main/shovill_contigs_graph | n/a |
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| shovill_logfile | #main/shovill_logfile | n/a |
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| tooldistillator_results_assembly | #main/tooldistillator_results_assembly | n/a |
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| tooldistillator_summarize_assembly | #main/tooldistillator_summarize_assembly | n/a |
|
Version History
v1.1.6 (latest) Created 17th May 2025 at 03:02 by WorkflowHub Bot
Updated to v1.1.6
Frozen
v1.1.6fe28724
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: 4759 Downloads: 1533 Runs: 1
Created: 18th Jun 2024 at 03:01
Last updated: 2nd Oct 2024 at 11:00
AttributionsNone
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