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
-
-
This has been addressed a few times before:
Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
--
Senthil Palanisami
-
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
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
68 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment