How do memory requirements scale with number of bases (or reads) for assemblies of 454 data on Newbler? I'm looking at sequencing a 3 GB genome to 7-8X coverage and doing a de novo assembly.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
kbrad,
Are you sure you want to do a human size genome (3Gbp) using 454? To even get to 8X coverage on this would require ~50 runs. (That would be ~$500,000 US at most places.) And typically one needs to go up to 20 - 25X coverage for true de novo assembly using 454.
Aside from these considerations I seriously doubt gsAssembler (newbler) could handle anything even close to 3Gbp.
-
Supposedly Assembler can handle up to 3Gbp genomes, as per their website. The manual says to contact your Roche rep if planning any assemblies >500Mbp.
I believe the memory requirement is 3bytes per read base, as per a Roche powerpoint from June 2009 (this may be different from the current version).
Comment
-
Roche 454's answer
I did learn from 454 tech support that 3 Gb genomes have been assembled with gsAssembler (Newbler) - including human. The memory requirements are 4 bytes per base to be assembled, so about 120 GB for 10x coverage of a 3 Gb genome.
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
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
66 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment