pox-virus-tiled-amplicon-ref-masking 2.0
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Run on GalaxyFrom a reference and a primer scheme generate two masked half-genome references for ITR-aware pox virus sequencing data analysis.
Associated Tutorial
This workflows is part of the tutorial Pox virus genome analysis from tiled-amplicon sequencing data, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Viktoria Isabel Schwarz, Wolfgang Maier
Tutorial Author(s): Wolfgang Maier, Tomas Klingström
Tutorial Contributor(s): Saskia Hiltemann, Helena Rasche, Wolfgang Maier, Anton Nekrutenko
Grants(s): BeYond-COVID, ELIXIR-CONVERGE, Addressing the dual emerging threats of African Swine Fever and Lumpy Skin Disease in Europe
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Primer Scheme | #main/Primer Scheme | The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b) |
|
| Reference FASTA | #main/Reference FASTA | The viral reference sequence to map sequenced reads against |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Select pool1 primers | Grep1 |
| 3 | Select pool2 primers | Grep1 |
| 4 | Compute sequence length | toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3 |
| 5 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2 |
| 6 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2 |
| 7 | Cut | Cut1 |
| 8 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
| 9 | Get start position of Pool2 | param_value_from_file |
| 10 | Get end position of sequence | param_value_from_file |
| 11 | Get end position of Pool1 | param_value_from_file |
| 12 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 13 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 14 | Mask Reference for Pool2 | toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0 |
| 15 | Mask Reference for Pool1 | toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| masked_ref_pool1 | #main/masked_ref_pool1 | n/a |
|
| masked_ref_pool2 | #main/masked_ref_pool2 | n/a |
|
Version History
master
Creators and Submitter
Views: 1367 Downloads: 180 Runs: 0
Created: 2nd Jun 2025 at 11:01
Tags AttributionsNone
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