There are great tools developed for detecting and genotyping STR expansions from short-read sequencing data.
It can identify expansions in various types of tandem repeats, including those associated with genetic diseases, like Fragile X, Huntington’s Disease, etc.
Some tools are: ExpansionHunter, Stripy, HipSTR, etc…
Is there any tool in galaxy that does something similar?
If anyone could walk with me on this task it would be of great help.
Hi @vergani
Galaxy community has a public software repository called Galaxy tool shed. Search it for repeat or any other relevant query. If tools you are interested in, are not present, you can suggest tools for wrapping here. Wrapper is a piece of code responsible for integration of a software into Galaxy environment. Add relevant post tags for tool wrapping requests.
Galaxy community has many public Galaxy servers, and some servers might have tools installed from private tool sheds. Maybe google Galaxy and “repeat expansion”. You also can check tools available on big public Galaxy servers, such as usegalaxy.org, usegalaxy.eu or usegalaxy.org.au. Galaxy has a search/filter box at the top of the tool panel.
Answering your question requires specialized knowledge, which I don’t have, hence, very general reply.
Kind regards,
Igor