quality-and-contamination-control/main
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Workflow Type: Galaxy
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Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input sequence reads (forward) | #main/Input sequence reads (forward) | Should be the forward strand of the paired end reads. |
|
| Input sequence reads (reverse) | #main/Input sequence reads (reverse) | Should be the reverse strand of the paired end reads. |
|
| Select a NCBI taxonomy database | #main/Select a NCBI taxonomy database | Select the ncbi taxonomy database for Recentrifuge. |
|
| Select a taxonomy database | #main/Select a taxonomy database | Select the database to use for assigning taxonomies for Kraken2 and Bracken. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | fastp_trimming_step | fastp_triming, quality analaysis and read cleaning toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
| 5 | kraken_taxonomy_assignation | kraken_taxonomy_assignation toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 |
| 6 | bracken_abundance_estimation | bracken_abundance_estimation toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.8+galaxy0 |
| 7 | recentrifuge_taxonomy_visualization | recentrifuge_taxonomy_visualization toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.14.0+galaxy0 |
| 8 | ToolDistillator | ToolDistillator extracts results from tools and creates a JSON file for each tool toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.8.5.0+galaxy0 |
| 9 | ToolDistillator summarize | ToolDistillator summarize groups all JSON file into a unique JSON file toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator_summarize/tooldistillator_summarize/0.8.5.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| 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_report_json | #main/fastp_report_json | n/a |
|
| fastp_trimmed_R1 | #main/fastp_trimmed_R1 | n/a |
|
| fastp_trimmed_R2 | #main/fastp_trimmed_R2 | 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 |
|
| tooldistillator_results | #main/tooldistillator_results | n/a |
|
| tooldistillator_summarize | #main/tooldistillator_summarize | n/a |
|
Version History
v1.1.9 (latest) Created 19th Jun 2025 at 03:01 by WorkflowHub Bot
Updated to v1.1.9
Frozen
v1.1.99c3de23
v1.0 (earliest) Created 20th Jun 2024 at 03:02 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
ba70f69
Creators and Submitter
Activity
Views: 8564 Downloads: 10476 Runs: 6
Created: 20th Jun 2024 at 03:02
Last updated: 2nd Oct 2024 at 10:54
AttributionsNone
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