Genome Assembly Paper in IEEE TPDS

A recent article in IEEE Transactions on Parallel and Distributed Computing describes our work in collaboration with the Notre Dame Bioinformatics Laboratory on SAND - The Scalable Assembler at Notre Dame .

In this article, we describe how to refactor the standard Celera genome assembly pipeline into a scalable computation that runs on thousands of distributed cores using the Work Queue . By explicitly handling the data dependencies between tasks, we are able to significantly improve runtime over Celera on a standard cluster. In addition this technique allows the user to break free of the shared filesystem and run on hundreds thousands of nodes drawn from clusters, clouds, and grids.