Repeat masking - TSI
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Run on GalaxyThis 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.
Frozen
Version-398500e0
Version 1.1 Created 8th May 2024 at 07:24 by Anna Syme
updated to include correct workflow report text
Frozen
Version-1.1
88bbd9c
Version 1 (earliest) Created 8th May 2024 at 04:59 by Anna Syme
Initial commit
Frozen
Version-1
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Created: 8th May 2024 at 04:59
Last updated: 20th Jun 2024 at 00:45
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https://orcid.org/0000-0002-9906-0673
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.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia, National Computational Infrastructure (NCI) WorkflowHub team
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/
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
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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
