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entropy 01-17-2010 08:04 PM

Computer hardare recommendations for assembly and annotation?
 
Hi all.

Just wondering what would be a reasonable workstation for assembling a 5.5bp bacterial genome? I'm leaning towards 454 rather than Illumina or SOLiD, but I assume the later two would need a lot more power due to the smaller reads... Any suggestions?

Thanks

flxlex 01-20-2010 12:01 PM

1 cpu, 4 GB memory would probably do the trick. Having more cpus will speed it up, though. This is assembly only, I don't know about annotation.

entropy 01-20-2010 12:39 PM

Quote:

Originally Posted by flxlex (Post 12695)
1 cpu, 4 GB memory would probably do the trick. Having more cpus will speed it up, though. This is assembly only, I don't know about annotation.

Ok. Good to know. Thanks!

mads b 03-15-2010 05:18 AM

We have been using a std 32bit desktop with 4gb RAM and open source software for bacterial genomes and Illumina reads. Itīs doable but some steps are 4-6 hours.

My current solution is a 64bit 2X XEON5500 quadrocore processors with 32 GB RAM. Commercial software (Genomic Workbench Clcbio). This is running smoothly and a de novo assembly of a bacterial genome is done in 10-15 min. My experience is: The faster the computer, the more likely you are to play around with parameters!


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