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Showing posts from March, 2011

de novo assembly of Illumina CEO genome in 11.5 h

THE initial aims of our group regarding de novo assembly of genomes were:

1. To assemble genomes using mixes of sequencing technologies simultaneously.
2. To assemble large repeat-rich genomes.
3. To devise novel approaches to deal with repeats.

1. To assemble genomes using mixes of sequencing technologies simultaneously.

We showed the feasibility of using mixes of sequencing technologies simultaneously using Ray -- a de novo genome assembler -- see Journal of Computational Biology 17(11): 1519-1533. Ray follows the Single Program, Multiple Data approach. It is implemented using the Message-Passing Interface.

With this method, a computation is separated into data-dependent parts. Each part is given to a processor and any processor communicates with others to access remote information.

2. To assemble large repeat-rich genomes.

It was thought that message transit in Ray would interfere strongly with the feasibility of genome assembly of large repeat-rich genomes…