Low Budget Workstation For Analysing Bacterial Illumina/454 Sequencing Data

Question

[shane.m.mclaughlin]

Hi,

I would like to build a workstation that is capable of analysing Illumina and 454 sequencing data from bacterial samples on a £2000 budget.

I am looking into parallel processing using GPUs, but any advice on which CPU would be suitable or how much RAM and hard disk space would be required would be greatly appreciated.

Thanks in advance,
Shane

[Dan D]

If you're truly on a small budget, why not just use a really cheap workstation and do all your work on the cloud? You could pay for your compute and storage needs as needed and get a lot more power than you would otherwise be able to acquire by purchasing physical hardware.

Answer 1

[JC]

Your answer depends on many factors, are you doing genomics? metagenomics? transcriptomics?

If you mainly will perfom asembly, GPUs are not necesary, the main factor is memory, at least 64 GB or more.

CPU is not a problem, you can find cheap 8+ cores, just be sure it's 64 bits.

Related:

workstations for NGS analysis?

What to do with 5-10K USD for computing equipment

[shane.m.mclaughlin]

Metagenomics if possible. I am pretty new to this and I'm currently working with the raw sequencing output from 454 sequencing, then OTU picking, assigning taxonomy and conducting diversity analyses using the 16S gene. My supervisor would like to start comparing more genes via Ilumina sequencing and our current workstation wouldn't be able to handle that. Thanks for replying!