GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data 1.0
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Run on GalaxyRemoval of human reads from SARS-CoV-2 sequencing data
Associated Tutorial
This workflows is part of the tutorial Removal of human reads from SARS-CoV-2 sequencing data, available in the GTN
Thanks to...
Tutorial Author(s): Wolfgang Maier
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input Dataset Collection | #main/Input Dataset Collection | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Trimmomatic | toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 |
| 2 | Unzip Collection | __UNZIP_COLLECTION__ |
| 3 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 |
| 4 | Samtools fastx | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
| 5 | Select | Grep1 |
| 6 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
| 7 | seqtk_subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 |
| 8 | seqtk_subseq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 |
| 9 | Paired-end collection of cleaned reads | __ZIP_COLLECTION__ |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Cleaned Data | #main/Cleaned Data | n/a |
|
| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
|
| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
master
Creators and Submitter
Views: 1253 Downloads: 173 Runs: 0
Created: 2nd Jun 2025 at 11:02
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Teams: Galaxy Training Network
Organizations: Galaxy
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