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

Changelog

[0.1]

Initial version of the RepeatMasking workflow for genomic sequencing data.

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/csbl/repeatmodeler/repeatmodeler/2.0.4+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.5+galaxy0