Question: De Novo Assembly
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gravatar for Cecilia Tamborindeguy
7.0 years ago by
Cecilia Tamborindeguy10 wrote:
Hello, I would like to know if Galaxy can do de novo assembly without a reference genome. Thanks. Cecilia
assembly • 2.1k views
ADD COMMENTlink modified 7.0 years ago by Peter Cock1.4k • written 7.0 years ago by Cecilia Tamborindeguy10
0
gravatar for Peter Cock
7.0 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k wrote:
On Thu, Sep 29, 2011 at 7:49 PM, Cecilia Tamborindeguy Are you trying to use the Public Galaxy or a local install? There are several assemblers with Galaxy Wrappers on the Galaxy ToolShed (e.g. Roche "Newbler", and MIRA 3) which you could add to your own local Galaxy if you have one. However, do novo genome assembly can be very computationally demanding, so not many Galaxy Instances will want to offer it. Peter
ADD COMMENTlink written 7.0 years ago by Peter Cock1.4k
Cecilia, There are wrappers for ABySS as well. These assemblers are generally for genome data. For transcriptome data, galaxy-central provides a wrapper for the Trinity assembler. If you don't want to/can't set up a local instance for assembly, consider using a cloud instance: http://wiki.g2.bx.psu.edu/Admin/Cloud Good luck, J.
ADD REPLYlink written 7.0 years ago by Jeremy Goecks2.2k
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