Forgive the forwarded email. Not used to working from an iPad.  

> On 2011-09-29, at 7:58 PM, Peter Cock <> wrote:
>> On Thu, Sep 29, 2011 at 7:49 PM, Cecilia Tamborindeguy
>> <> 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
> I would like to echo Peter's advice. (Again, that's twice in 5 min from 2 
> different lists. I promise you I'm not stalking you, Peter). 
> Genome assembly is a bit of a dedicated domain with respect to expertise and 
> time. If possible, if you are assembling a lot of genome data, you really 
> should set yourself up properly with a multiple-CPU unix box with a lot of 
> RAM and dedicate it to assembly. Install MIRA, Newbler, Velvet, AMOS, 
> samtools, bamtools, bedtools, Staden, phred/phrap/consed on it, and you can 
> assemble and interconvert data to your heart's content. 
> Galaxy is a wonderful and useful service but assembling genomes does require 
> dedicated power and expertise, and preferably in house. I just forked out for 
> a 64 CPU processor with 1 TB RAM bc we assemble lots of genomes. You don't 
> have to go that far but a 3-4 quad processor box with 128 GB RAM and 1 TB 
> disk should be on your mind. 
> John
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