repeatmasking/main v0.1
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This workflow uses RepeatModeler and RepeatMasker for genome analysis.
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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.
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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 |
|
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 |
|
| RepeatMasker output log | #main/RepeatMasker output log | n/a |
|
| RepeatMasker repeat annotation | #main/RepeatMasker repeat annotation | n/a |
|
| RepeatMasker repeat catalog | #main/RepeatMasker repeat catalog | n/a |
|
| RepeatMasker repeat statistics | #main/RepeatMasker repeat statistics | n/a |
|
| RepeatModeler consensus sequences | #main/RepeatModeler consensus sequences | n/a |
|
| RepeatModeler seeds alignments | #main/RepeatModeler seeds alignments | n/a |
|
Version History
v0.1 (earliest) Created 22nd Sep 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
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v0.1e62a6ee
Creators and SubmitterViews: 6231 Downloads: 1890 Runs: 0
Created: 22nd Sep 2023 at 03:01
Last updated: 18th Aug 2025 at 16:41
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EuroScienceGateway will leverage a distributed computing network across 13 European countries, accessible via 6 national, user-friendly web portals, facilitating access to compute and storage infrastructures across Europe as well as to data, tools, workflows and services that can be customized to suit researchers’ needs.EuroScienceGateway will deliver a robust, scalable, seamlessly integrated open infrastructure for data-driven research, contributing an innovative and customizable service for ...
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Collection of workflows used or developed by the EuroScienceGateway project.
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