SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
qPCR reagent recommendation HICORE Sample Prep / Library Generation 2 08-29-2011 01:55 PM
GATK Recommendation. kasthuri Bioinformatics 0 06-08-2011 01:05 PM
Server hardware and OS jdjax Bioinformatics 12 01-14-2011 06:18 PM
intro/review recommendation DPB Literature Watch 3 08-12-2009 01:37 PM
Sonicator recommendation monad Illumina/Solexa 1 02-02-2009 08:18 AM

Reply
 
Thread Tools
Old 02-20-2013, 11:40 AM   #1
lkral
Member
 
Location: Carrollton, GA

Join Date: May 2011
Posts: 27
Default 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 is offline   Reply With Quote
Old 02-21-2013, 08:32 AM   #2
lkral
Member
 
Location: Carrollton, GA

Join Date: May 2011
Posts: 27
Default

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?

Last edited by lkral; 02-22-2013 at 04:56 PM.
lkral is offline   Reply With Quote
Old 07-19-2013, 04:56 PM   #3
jlli2000
Junior Member
 
Location: california

Join Date: Jan 2010
Posts: 4
Default Mac vs Linux computer for MiSeq

Hello,

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

I found one at apple.com

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
Hardware
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?

Thanks,
jlli2000 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO