de novo assembler for 50 million reads on a desktop machine

[KevinLam]

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]

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]

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/whitepapers/technical_note_on_alpha_version_of_de_novo_assembly_on_the_CLC_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***************