This isn't an easy question to answer. Here's why:

*there is significant variation in mammalian genome size; of course, larger 
genomes require more resources, but the relationship is difficult to quantify;
*assembly can take anywhere from a day to a week depending on software and 
resource choices;
*variant detection can take anywhere from 1-4 days depending on software used;
*completing assembly and variant detection in 48 hours is something that is 
challenging for even the most advanced genomics labs.

To answer your question, I'd start with 256-512GB of RAM on a machine and 36-72 
compute cores across a cluster. This is simply a guess of course. Before 
investing in hardware, you might try your analysis on the cloud ( 
usegalaxy.org/cloud ) to get a sense of the resources needed.

Good luck,
J.

On Sep 11, 2013, at 8:34 AM, Gerald Bothe wrote:

> Can I put in a similar question on top of this: How much resources do you 
> need for re-sequencing of a mammalian genome (assembly and variant 
> detection), one job at a time? E.g. how much RAM  etc. if I want the 
> re-sequencing SAM file of a 30-fold coverage be done in 48 hours?
>  
> Gerald
>  
> Gerald Bothe
> 32 Plum Hill Road
> East Lyme, CT 06333
> (860) 451 8776
> 
> From: Nikos Sidiropoulos <nikos.sid...@gmail.com>
> To: Peter Cock <p.j.a.c...@googlemail.com> 
> Cc: "<galaxy-...@bx.psu.edu>" <galaxy-...@bx.psu.edu> 
> Sent: Wednesday, September 11, 2013 8:19 AM
> Subject: Re: [galaxy-dev] Scaling and hardware requirements
> 
> Hi Peter
> 
> It's going to be one big machine, running both Galaxy server and the jobs. 
> It's going to be a multi-process configuration. If that idea is terribly bad 
> please let me know so I can give back the feedback. 
> 
> De novo assembly can also be for the human/mouse genome. 
> 
> Bests,
> Nikos
> 
> 
> 2013/9/11 Peter Cock <p.j.a.c...@googlemail.com>
> On Wed, Sep 11, 2013 at 1:03 PM, Nikos Sidiropoulos
> <nikos.sid...@gmail.com> wrote:
> > Hi all,
> >
> > I have a couple of questions regarding a server setup dedicated on Galaxy.
> >
> > The idea is to buy a 64 core 256GB RAM server. From my experience I believe
> > that Galaxy will be able to scale up to 64 cpu's but I would like some more
> > feedback on this. Also, is 4GB RAM per CPU core enough for NGS data?
> > (including de-novo assembly)
> >
> > Bests,
> > Nikos
> 
> Hi Nikos,
> 
> Is this going to be one server both for running Galaxy (which
> needs fairly low resources) and running jobs for Galaxy,
> like de novo assemblies (which need high resources)?
> 
> i.e. You have one big machine only, no cluster?
> 
> For de novo assembly the RAM per core/CPU isn't important,
> it is the total RAM on the machine. How much RAM you
> need depends on which assembler you use, the organism
> (both size and also complexity) and the volume of data.
> 
> What you've described should be fine for bacterial assemblies
> and smaller eukaryotes - beyond that you'll need to give
> more details.
> 
> Peter
> 
> 
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