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lkral 02-20-2013 11:40 AM

GOSSAMER hardware recommendation?
I will need to assemble a genome from two PE250 MiSeq runs generating a total of about 12 to 14 Gbp of sequence. Based on some preliminary alignments to genes I had previously cloned and sequenced this would, on average, be better than 10x coverage. Since I don't have access to or funds for time on a computer with sufficient RAM to run something like Velvet, I was looking at Gossamer as an assembler with low hardware resource requirements. My question is this. I may be able to configure a VM for a short amount of time and I am wondering what would be a reasonable amount of vRAM and minimum number of CPU cores to get the assembly done in a reasonable time period.

lkral 02-21-2013 08:32 AM

I missed this somehow, but the Gossamer readme file says:

"Mammalian size genomes have been assembled using goss on a 32 GB Ubuntu machine."

So, since the genome I'll be assembling is about 1 Gbp, I should think that 32 GB of vRAM should be sufficient. If anyone has experience assembling with Gossamer, would there be any advantage to try and up that to 64 GB of RAM?

jlli2000 07-19-2013 04:56 PM

Mac vs Linux computer for MiSeq

Can anyone tell if a MacPro is good enough for a basic MiSeq application anaysis?

I found one at

Mac Pro: 12-Core
Item Price: $4,649.00 Quantity (Mac Pro: 12-Core) Line Price:$4,649.00
Remove (Mac Pro: 12-Core) Save (Mac Pro: 12-Core)
Part number: Z0P2
Available to ship: 2-4 business days
Two 2.40GHz 6-Core Intel Xeon processors (12 cores)
32GB (8x4GB)
2TB 7200-rpm Serial ATA 3Gb/s hard drive
ATI Radeon HD 5770 1GB

Is this good enough?


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