Repeat masking - TSI
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Run on usegalaxy.euThis 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 = 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.
- 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 |
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 1.1 (latest) Created 8th May 2024 at 07:24 by Anna Syme
updated to include correct workflow report text
Frozen
Version-1.188bbd9c
Version 1 (earliest) Created 8th May 2024 at 04:59 by Anna Syme
Initial commit
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Version-1
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Created: 8th May 2024 at 04:59
Last updated: 9th May 2024 at 05:00
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The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
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Web page: https://www.biocommons.org.au/
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
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Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
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
