Computer for running GS Junior Software

[Martin Mikkelsen]

Dear all,

We just bought a GS Junior at my lab. We are planning to do most of the data analysis outside the lab and away from the computer that comes with the instrument.

Since my computer is more or less outdated I am getting a new one.

Is there anything I special I should be aware of. Is a powerfull prosessor needed etc.?

Currently I am thinking of a computer with a very big hardrive and having the Centos Linux installed on the machine.

Hope anyone has some suggestions or experience with it.

Thanks!

[Zaag]

As much as RAM as possible and a quadcore is nice for mapping but useless for assembly, so that depends on the experiments you are planning.

[Martin Mikkelsen]

Hi Zaag,

Thanks for your reply.

The plan is mostly shotgun de novo sequencing, so I guess quadcore is not that important?

[Zaag]

No, it is always nicer for post-assembly processes because it is generally faster. But it is not that important.

Edit: however, when you have assembled a reference genome you might want to do some mapping so if affordable I would always go for a quadcore.

[Martin Mikkelsen]

So as for anything in life, the bigger the better :-)

[martin2]

No, even for assembly number of CPU cores does matter, try setting the number of CPUs to 1 and you see the difference, compared to 4!

Buy a CPU with highest frequency, rather than quad-core take dual-core and yes, 8GB RAM is a minimum, I'd go for 16GB immediately, if not more.

Configure the 2 disks in a raid-mirroring mode and have a third drive from /var/tmp. Finally, change the environment variable so that it points to the fast, non-RAID drive, e.g. GS_CACHEDIR=/var/tmp . It is in the docs. ;-)

[drio]

What kind of genomes are you planning to denovo assembly? If working with mammals you are going to need a very decent amount of memory 128G minimum. Perhaps 64G would work if you use partitioning. Anyone has experience with that?

[Jacky76]

Computer examples for data rig

There are some estimation of the computer specification for data analysis.
Please perfer the attached table. You may be able to guess better about the spec of your off rig for your special application and the size, number of yours.
I guess you have GS Junior, so you will not analyze human genome. As I know GS Mapper and Assembler can cover human genome, but the concern is the computer to support. With the similar spec with GS Junior desktop, you may be able to do the most of your applications. If you want to install Windows for OS on your off-rig for analysis, you can use 3rd party software like VMPlayer that will enable remote access to Linux on Windows.

Please refer to below examples.

Usage level Suitable for Example System

Minimum DataRig
_ Mapping and assembly of genomes up to 10 M bases
_ Small amplicon projects (dozens of multiplexed amplicons with limited variation)
Dell PowerEdge 1950 (rack mount),
Dell Precision 490 (workstation), or similar
_ Single Dual Core 3.00 GHz x86 64-bit
Xeon processor
_ 4 GB of RAM
_ 500 GB of hard disk space in either RAID 1 or 5 (both SAS and SATA disks are acceptable.)

General Purpose DataRig
_ Assembly of genomes up to 35 M bases
_ Mapping of genomes up to 1.5 G bases
_ Substantial amplicon projects
(100-200 multiplexed amplicons with high variation)
Dell PowerEdge 2900 (rack mount or workstation), or similar
_ Two Dual Core 3.00 GHz x86 64-bit Xeon processors
_ 8 GB of RAM
_ 1 TB of hard disk space in RAID 5 (both SAS and SATA disks are acceptable.)

High-End DataRig
_ Assembly of genomes up to 50 M bases
_ Mapping of genomes up to 3 G bases
_ Substantial amplicon projects (200-400 multiplexed amplicons with high variation).
Dell PowerEdge 2900 (rack mount or workstation), or similar
_ Two Quad Core 2.66 GHz x86 64-bit Xeon processors
_ 16 GB of RAM
_ 2 TB of disk space in RAID 5 (both SAS and SATA disks are acceptable.)

And if you consider compatible use of 454 software, you had better to install below Linux version. There are two kinds of RedHat, one is commercial and the other one is freeware. The freeware version is okay.

Red Hat Enterprise Linux 4 or 5 × 64