de novo assembler for 50 million reads on a desktop machine

KevinLam · 12-02-2009, 01:22 AM

Does anyone know if such a software exists?
Soft genetics nextgene can do 10 million reads on a 8Gb Ram desktop are there others out there? commercial or open source

colindaven · 12-02-2009, 06:20 AM

The best and easiest I ve found so far is Velvet.

50m reads on an 8Gb machine is probably pushing it though.

Otherwise, Edena is ok, and I had issues installing Abyss on linux.

col

Roald · 12-03-2009, 04:12 AM

Hi Kevin,

We are about to release a beta-version of our new de novo assembler which is able to assemble large amounts of data on modest hardware. Data can be combined from various platforms and protocols.
You can read more about the specs here:
http://www.clcbio.com/index.php?id=1413
http://www.clcbio.com/files/whitepap...C_NGS_Cell.pdf

Although the benchmarks are made with 30+ Gb RAM it runs nicely on 8 Gb machines as well for the data amount you mentioned.

Cheers

Roald Forsberg

**************Disclaimer: I work for CLC bio***************

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12-02-2009, 01:22 AM	#1
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 203	de novo assembler for 50 million reads on a desktop machine Does anyone know if such a software exists? Soft genetics nextgene can do 10 million reads on a 8Gb Ram desktop are there others out there? commercial or open source

12-02-2009, 06:20 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	The best and easiest I ve found so far is Velvet. 50m reads on an 8Gb machine is probably pushing it though. Otherwise, Edena is ok, and I had issues installing Abyss on linux. col

12-03-2009, 04:12 AM	#3
Roald Director at CLC bio Location: Denmark Join Date: Aug 2008 Posts: 26	Hi Kevin, We are about to release a beta-version of our new de novo assembler which is able to assemble large amounts of data on modest hardware. Data can be combined from various platforms and protocols. You can read more about the specs here: http://www.clcbio.com/index.php?id=1413 http://www.clcbio.com/files/whitepap...C_NGS_Cell.pdf Although the benchmarks are made with 30+ Gb RAM it runs nicely on 8 Gb machines as well for the data amount you mentioned. Cheers Roald Forsberg ************Disclaimer: I work for CLC bio*************