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 = 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
  • 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
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
  • 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 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-3 98500e0

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 571d961
help Creators and Submitter
Creators
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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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Created: 8th May 2024 at 04:59

Last updated: 20th Jun 2024 at 00:45

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