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Method Article
Matthew Berriman
Berriman Lab Group, Sanger Institute
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
It is useful to mask repeat elements within the assembly of a newly sequenced genome for tasks such as gene-finding, but also for the purpose of understanding evolution of repetitive elements. To do this, one must first construct a library of the repeat elements in the genome. We present a protocol for creating a comprehensive repeat library for the genome of a newly sequenced parasitic worm, based on merging repeat libraries made by RepeatModeler, TransposonPSI and LTRharvest.
Keywords
repeat-finding, repeat library, repeat libraries, RepeatMasker, RepeatModeler, Transposon PSI, LTRharvest, LTRdigest, transposons, transposable elements, repetitive elements, repetitive DNA, repeats, parasites, genomes, assemblies, parasitic worms, helminths, nematodes, flatworms, platyhelminths, Nematoda, Platyhelminthes
The authors declare no competing financial interests.
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An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Matthew Berriman
Berriman Lab Group, Sanger Institute
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 14 May, 2018
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
It is useful to mask repeat elements within the assembly of a newly sequenced genome for tasks such as gene-finding, but also for the purpose of understanding evolution of repetitive elements. To do this, one must first construct a library of the repeat elements in the genome. We present a protocol for creating a comprehensive repeat library for the genome of a newly sequenced parasitic worm, based on merging repeat libraries made by RepeatModeler, TransposonPSI and LTRharvest.
The authors declare no competing financial interests.
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