Computer hardare recommendations for assembly and annotation?

entropy · 01-17-2010, 08:04 PM

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

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. It´s 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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01-17-2010, 08:04 PM	#1
entropy Junior Member Location: Canada Join Date: Jan 2010 Posts: 6	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

01-20-2010, 12:01 PM	#2
flxlex Moderator Location: Oslo, Norway Join Date: Nov 2008 Posts: 415	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.

03-15-2010, 05:18 AM	#4
mads b Junior Member Location: Copenhagen Join Date: Aug 2009 Posts: 4	We have been using a std 32bit desktop with 4gb RAM and open source software for bacterial genomes and Illumina reads. It´s 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!