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Old 01-17-2010, 08:04 PM   #1
entropy
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Default 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
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Old 01-20-2010, 12:01 PM   #2
flxlex
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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.
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Old 01-20-2010, 12:39 PM   #3
entropy
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Quote:
Originally Posted by flxlex View Post
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!
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Old 03-15-2010, 05:18 AM   #4
mads b
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We have been using a std 32bit desktop with 4gb RAM and open source software for bacterial genomes and Illumina reads. Its 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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