Forgive the forwarded email. Not used to working from an iPad.
On 2011-09-29, at 7:58 PM, Peter Cock
> On Thu, Sep 29, 2011 at 7:49 PM, Cecilia Tamborindeguy
> <ctamborindeguy(a)ag.tamu.edu> wrote:
>> I would like to know if Galaxy can do de novo assembly without a reference
> 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.
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
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.