Workflow Type: Galaxy

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 = 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
  • File

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
  • File
output_log #main/output_log n/a
  • File
output_masked_genome #main/output_masked_genome n/a
  • File
output_repeat_catalog #main/output_repeat_catalog n/a
  • File
seeds #main/seeds n/a
  • File
sequences #main/sequences n/a
  • File

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-1.1 88bbd9c

Version 1 (earliest) Created 8th May 2024 at 04:59 by Anna Syme

Initial commit


Frozen Version-1 571d961
help Creators and Submitter
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Citation
Silver, L., & Syme, A. (2024). Repeat masking - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.875.2
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Views: 326

Created: 8th May 2024 at 04:59

Last updated: 9th May 2024 at 05:00

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