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.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
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, 05:56 PM.
-
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,
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 08:47 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Today, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
59 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
Comment