Workflow Type: Galaxy
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This is part of a series of workflows to annotate a genome, tagged with TSI-annotation
.
These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.
The workflows can be run in this order:
- Repeat masking
- RNAseq QC and read trimming
- Find transcripts
- Combine transcripts
- Extract transcripts
- Convert formats
- Fgenesh annotation
Workflow information:
- Input = genome.fasta.
- Outputs = soft_masked_genome.fasta, hard_masked_genome.fasta, and table of repeats found.
- Runs RepeatModeler with default settings, uses the output of this (repeat library) as input into RepeatMasker.
- Runs RepeatMasker with default settings except for: Skip masking of simple tandem repeats and low complexity regions. (-nolow) : default set to yes. Perform softmasking instead of hardmasking - set to yes.
- Converts the soft-masked genome to hard-masked for for use in other tools if required.
- Workflow report displays an edited table of repeats found. Note: a known bug is that sometimes the workflow report text resets to default text. To restore, look for an earlier workflow version with correct workflow report text, and copy and paste report text into current version.
Inputs
ID | Name | Description | Type |
---|---|---|---|
genome.fasta | #main/genome.fasta | n/a |
|
Steps
ID | Name | Description |
---|---|---|
1 | RepeatModeler | toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1 |
2 | RepeatMasker | toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0 |
3 | Convert soft-masking to hard-masking | Replace all lowercase (except in headers) with Ns toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Repeats_output_table | #main/Repeats_output_table | n/a |
|
output_log | #main/output_log | n/a |
|
output_masked_genome | #main/output_masked_genome | n/a |
|
output_repeat_catalog | #main/output_repeat_catalog | n/a |
|
seeds | #main/seeds | n/a |
|
sequences | #main/sequences | n/a |
|
Version History
Version 3 (latest) Created 20th Jun 2024 at 00:41 by Anna Syme
Added in additional step to convert soft-masking to hard-masking, for use in other tools.
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Version-3
98500e0
Version 1.1 Created 8th May 2024 at 07:24 by Anna Syme
updated to include correct workflow report text
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Version-1.1
88bbd9c
Version 1 (earliest) Created 8th May 2024 at 04:59 by Anna Syme
Initial commit
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Version-1
571d961
Creators and Submitter
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Citation
Silver, L., & Syme, A. (2024). Repeat masking - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.875.3
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Views: 2313 Downloads: 430 Runs: 0
Created: 8th May 2024 at 04:59
Last updated: 20th Jun 2024 at 00:45
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