RepeatMasking Workflow
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 |
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Steps
ID | Name | Description |
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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 |
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RepeatMasker masked genome | #main/RepeatMasker masked genome | n/a |
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RepeatMasker output log | #main/RepeatMasker output log | n/a |
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RepeatMasker repeat annotation | #main/RepeatMasker repeat annotation | n/a |
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RepeatMasker repeat catalog | #main/RepeatMasker repeat catalog | n/a |
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RepeatMasker repeat statistics | #main/RepeatMasker repeat statistics | n/a |
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RepeatModeler consensus sequences | #main/RepeatModeler consensus sequences | n/a |
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RepeatModeler seeds alignments | #main/RepeatModeler seeds alignments | n/a |
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Version History
v0.1 (earliest) Created 22nd Sep 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
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v0.1
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Created: 22nd Sep 2023 at 03:01
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