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Old 05-29-2009, 05:22 PM   #1
AnthonyB
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Default SOAPdenovo

Has anyone tried the new SOAPdenovo program for assembling short reads and compared it to velvet etc? Their website claims that it can assemble human-sized genomes (eg panda) without crazy-high RAM (~150Gb) requirements.
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Old 05-29-2009, 10:27 PM   #2
GerryB
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Actually their website says the opposite.

Quote:
Originally Posted by SOAP site
SOAPdenovo aims for large plant and animal genomes, although it also works well on bacteria and fungi genomes. It runs on 64-bit Linux system with a minimum of 5G physical memory. For big genomes like human, about 150 GB memory would be required.
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Old 05-30-2009, 06:12 PM   #3
AnthonyB
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I guess I should have been clearer in my post to say that the 150GB RAM requirement of SOAPdenovo for a human sized genome seems to be much lower than estimates I've seen for other short read de novo programs (>500GB RAM).
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