I was asked to get an estimate of how much memory it realistically takes to run Velvet to assemble a large genome, e.g. human genome size. If anybody had some idea or experience it would be a help. Even if you have experience with Velvet and a genome in the 100's of mb range, it could be helpful. I would guess roughly 20X coverage may be a reasonable size to consider, but it could take more to really assemble a genome successfully from small reads.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
spenthil ist right, check first if there is already some information that helps you.
And there is an velvet mailing list, http://listserver.ebi.ac.uk/mailman/...o/velvet-users where zerbino is also very active.
The RAM you need depends a lot on the kmer (hash) you choose. Normally the higher your coverage and your minimum read length the higher kmer (hash) you can choose and therefore less RAM you will need. For a human genome depending on the quality of your reads you will still need around 64 - 128GB RAM.
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 07:03 AM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Today, 07:03 AM
|
||
Started by seqadmin, 05-10-2024, 06:35 AM
|
0 responses
31 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
41 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
33 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
Comment