Talk:Wikiomics:Repeat finding: Difference between revisions
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== REPET == | == REPET == | ||
http://urgi.versailles.inra.fr/index.php//Tools/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 | |||
Latest revision as of 17:26, 14 January 2016
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
