Talk:Wikiomics:Repeat finding

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RepeatScout possible speedups: 

RepeatMasker  input_genome_sequence.fas -lib output_repeats.fas.filtered_1 -norna -nolow -no_is

-qq (5-10x faster, a bit less sensitive) -pa numbers of parallel processes to use, in case you got multiprocessor or multicore machines

If one is concerned about lower sensitivity of "-qq", then this can be compensated by lowering minimum occurrence threshold (i.e. ("--thresh=5) in the next step.

  • darked 09:26, 23 March 2010 (EDT):

Seedmasker

"SeedMasker is public domain software for masking genomes based on over-represented words." http://www.drive5.com/seedmasker/

  • darked 15:30, 24 March 2010 (EDT):

ReRep

GSS sequences including 454 data


http://www.biomedcentral.com/1471-2105/9/366/

http://bioinfo.pdtis.fiocruz.br/ReRep/

Tandem repeat finder parser

@SOURCEFORGE PERL script 2 check http://sourceforge.net/projects/trfparser/


REPET

http://urgi.versailles.inra.fr/index.php//Tools/REPET

TANTAN

new algorithm from 2011:

www: http://www.cbrc.jp/tantan/

article: http://nar.oxfordjournals.org/content/39/4/e23.full

RepARK

http://nar.oxfordjournals.org/content/early/2014/03/14/nar.gku210.full

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