Hello, I would like to know if Galaxy can do de novo assembly without a reference genome. Thanks. Cecilia
On Thu, Sep 29, 2011 at 7:49 PM, Cecilia Tamborindeguy ctamborindeguy@ag.tamu.edu wrote:
Hello,
I would like to know if Galaxy can do de novo assembly without a reference genome.
Thanks.
Cecilia
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
Cecilia,
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.
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.
However, do novo genome assembly can be very computationally demanding, so not many Galaxy Instances will want to offer it.
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.
galaxy-user@lists.galaxyproject.org
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Cecilia Tamborindeguy -
Jeremy Goecks -
Peter Cock