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Question: Are there Structural Variant Analysis Software in Galaxy?
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gravatar for orlando.wong
2.4 years ago by
orlando.wong • 10
orlando.wong • 10 wrote:

Hello Galaxy,

Do you know which software available on Galaxy is capable of performing structural variant analysis, for large insertions, deletions, inversions, translocations, etc.

I found under the tab, NGS:Variant Analysis, a few programs for variant analysis, except these deal with a smaller scale like SNPs and indels. I am unsure if those software algorithms are able to detect inversions or other structural variants.

I have tried using software for structural variant analysis from the command line. Pindel, LUMPY, breakdancer , SVDetect, but I am having issues with compiling and building them from source, even with the aid of Google, stackoverflow, biostars, and github, possibly because they were intended for use on UNIX or LINUX, and I am using Cygwin on Windows and an OS X.

Thanks!
structural variant ngs galaxy • 960 views
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modified 2.4 years ago by solo7773 • 20 • written 2.4 years ago by orlando.wong • 10
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gravatar for solo7773
2.4 years ago by
solo7773 • 20
solo7773 • 20 wrote:

Sorry I have no good answer for your question. But since you are using Cygwin on Windows and you also know how to use OS X, why not install a virtual machine software, e.g. virtual box, on your windows and then install a Linux OS (like Ubuntu) as a virtual machine within virtual box, and then you can enjoy a nearly original Linux environment. After that, you will solve the compiling problem on Cygwin.

By the way, if the public galaxy site doesn't offer such tool but a local version does, you still need a Linux OS to install a local galaxy and then install that tool from the galaxy toolshed.
ADD COMMENT • link modified 2.4 years ago • written 2.4 years ago by solo7773 • 20

Hi solo7773,

Is it possible for me to install a tool from the galaxy toolshed onto the public galaxy servers? We do not have the computer power and resources to run our own local galaxy.

Thanks!

ADD REPLY • link written 2.4 years ago by orlando.wong • 10
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