phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.MOTIVATION
 phRAIDER is a de novo TE identification tool that address the issues of excessive runtime without sacrificing sensitivity as compared to competing tools.  As compared with the premier tool in the literature, RepeatScout, phRAIDER shows an average 10× speedup on any single human chromosome and has the ability to process the whole human genome in just over three hours.  phRAIDER is an open source tool available from https://github.com/karroje/phRAIDER CONTACT: : karroje@miamiOH.edu or



phRAIDER
Although RepeatMasker and nHMMER are useful for identifying these repeats, they require a pre-compiled repeat library-which is not always available. 
RepeatMasker
Although RepeatMasker and nHMMER are useful for identifying these repeats, they require a pre-compiled repeat library-which is not always available. 
nHMMER
De novo identification tools such as Recon, RepeatScout or RepeatGluer serve to identify TEs purely from sequence content, but are either limited by runtimes that prohibit whole-genome use or degrade in quality in the presence of substitutions that disrupt the sequence patterns.



Recon
De novo identification tools such as Recon, RepeatScout or RepeatGluer serve to identify TEs purely from sequence content, but are either limited by runtimes that prohibit whole-genome use or degrade in quality in the presence of substitutions that disrupt the sequence patterns.


 As compared with the premier tool in the literature, RepeatScout, phRAIDER shows an average 10× speedup on any single human chromosome and has the ability to process the whole human genome in just over three hours. 
RepeatScout
De novo identification tools such as Recon, RepeatScout or RepeatGluer serve to identify TEs purely from sequence content, but are either limited by runtimes that prohibit whole-genome use or degrade in quality in the presence of substitutions that disrupt the sequence patterns.



RepeatGluer