Workflow Type: Galaxy

RepeatMasking Workflow

This workflow uses RepeatModeler and RepeatMasker for genome analysis.

  • RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.

  • RepeatMasker is a program that analyzes DNA sequences for interleaved repeats and low-complexity DNA sequences. The result of the program is a detailed annotation of the repeats present in the query sequence, as well as a modified version of the query sequence in which all annotated repeats are present.

Input dataset for RepeatModeler

  • RepeatModeler requires a single input file, a genome in fasta format.

Outputs dataset for RepeatModeler

  • Two output files are generated:
    • summary file (.tbl)
    • fasta file containing alignments in order of appearance in the query sequence

Input dataset for RepeatMasker

  • ReapatMasker requires the fasta file generated by RepeatModeler

Outputs datasets for RepeatMasker

  • Five output files are generated:
    • a fasta file
    • .gff3 file
    • a table summarizing the repeated content of the sequence analyzed
    • a file with statistics related to the repeated content of the sequence analyzed
    • a summary of the mutation sites found and the order of grouping

Inputs

ID Name Description Type
input #main/input 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
RepeatMasker masked genome #main/RepeatMasker masked genome n/a
  • File
RepeatMasker output log #main/RepeatMasker output log n/a
  • File
RepeatMasker repeat annotation #main/RepeatMasker repeat annotation n/a
  • File
RepeatMasker repeat catalog #main/RepeatMasker repeat catalog n/a
  • File
RepeatMasker repeat statistics #main/RepeatMasker repeat statistics n/a
  • File
RepeatModeler consensus sequences #main/RepeatModeler consensus sequences n/a
  • File
RepeatModeler seeds alignments #main/RepeatModeler seeds alignments n/a
  • File

Version History

v0.1 (earliest) Created 22nd Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 e62a6ee
help Creators and Submitter
Creator
  • Romane Libouban
Submitter
License
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Views: 1550

Created: 22nd Sep 2023 at 03:01

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