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
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, 04-25-2024, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
04-25-2024, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
62 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment