CLC genomics server for assembling large genomes

ngs_agd · 03-20-2012, 05:01 AM

Has anybody tried using CLCBio Genomics server for assembling large genomes (Panda, Human etc)?

We have interest in assembling large genomes with small amount of RAM. Tried using CLCBio server based on their claims, but we were not able to do de novo assembly of panda (from Li et al Nat Gen 2010) and Human (from SRA) reads generated on Illumina platform.
Our server configuration is 128 GB RAM and 2 Intel quad cores.
We ran the assembly (both contig generation and mapping) with all default parameters.

We would like to hear if anybody has had similar or maybe better experience.

maubp · 03-20-2012, 06:52 AM

I know some of my colleagues have had some success with the "CLCBio Assembly Cell" (or whatever their command line assembly tool is called) with plant genomes. Success meaning getting any useful contigs from a de novo assemblies, compared to most tools which needed too much RAM to do anything.

Sorry I can't be more detailed.

NextGenSeq · 03-20-2012, 02:36 PM

I was able to de novo assemble a 2GB genome pretty well with 24GB of RAM.

ngs_agd · 03-20-2012, 08:29 PM

Quote:

Originally Posted by NextGenSeq

I was able to de novo assemble a 2GB genome pretty well with 24GB of RAM.

Can you please elaborate on this? What was the organism, how much data did you provide, the platform on which the data was generated, how long it took to complete the assembly etc. Greatly appreicate your response.

NextGenSeq · 03-23-2012, 12:47 PM

It took a week with 350 million reads. Anymore than this you need more RAM. It's not published yet so can't say the organism besides it's vertebrate.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Avadis NGS vs CLC Genomics?	Novice	Bioinformatics	32	09-19-2013 12:56 PM
CLC Genomics Workbench	ECO	Bioinformatics	65	03-27-2012 04:05 AM
tools for assembling large contigs	shuang	Bioinformatics	2	02-29-2012 11:08 PM
Assembling very large reads	k-gun12	Bioinformatics	2	03-12-2011 08:06 AM
CoComputational Resources on Assembling Genomes	raghavagps	Bioinformatics	0	01-17-2010 09:56 AM

03-20-2012, 05:01 AM	#1
ngs_agd Junior Member Location: India Join Date: Feb 2011 Posts: 7	CLC genomics server for assembling large genomes Has anybody tried using CLCBio Genomics server for assembling large genomes (Panda, Human etc)? We have interest in assembling large genomes with small amount of RAM. Tried using CLCBio server based on their claims, but we were not able to do de novo assembly of panda (from Li et al Nat Gen 2010) and Human (from SRA) reads generated on Illumina platform. Our server configuration is 128 GB RAM and 2 Intel quad cores. We ran the assembly (both contig generation and mapping) with all default parameters. We would like to hear if anybody has had similar or maybe better experience.

03-20-2012, 06:52 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,300	I know some of my colleagues have had some success with the "CLCBio Assembly Cell" (or whatever their command line assembly tool is called) with plant genomes. Success meaning getting any useful contigs from a de novo assemblies, compared to most tools which needed too much RAM to do anything. Sorry I can't be more detailed.

03-20-2012, 02:36 PM	#3
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 382	I was able to de novo assemble a 2GB genome pretty well with 24GB of RAM.

03-23-2012, 12:47 PM	#5
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 382	It took a week with 350 million reads. Anymore than this you need more RAM. It's not published yet so can't say the organism besides it's vertebrate.