Which Tools do you use for (Tandem) Repeat Detection? Why?

[voidnyx]

Hi,

I recently started my work for a university project where I want to analyze repetetive sequences in genomic DNA of two closely related species. This contains things like larger, further away Repeats but also short tandem repeats. I have no prior experience with this and have read some papers to start with.

I found there are a handful of programs for Tandem Repeat detection like TRF, Mreps, ATRhunter, RepeatMasker and so on. Based on different approaches and different opinions i could not really see a consensus in the articles i read on which program to use, not even on distinct (dis)advantages.

What i took away from them was, you have to be extra careful with your parameter settings for most of the programs and basically have to be author of the program to actually understand whats happening. Bottom line I am pretty confused about what to use.



So I would like to hear opinions from people who actually use some kind of Repeat Detection software on this topic or have experience with the matter. Which programs you think are good? and where do you see their advantages or disadvantages?

Thanks for any input.

[GenoMax]

Also on Biostars: https://www.biostars.org/p/147548/