A team of multi-institutional researchers has streamlined and accelerated genome assembly from a months-long process to minutes via the development of Meraculous, a tool created using algorithms, computational methods, and the Unified Parallel C (UPC) programming language.
"Using the parallelized version of Meraculous, we can now assemble the entire human genome in about eight minutes using 15,360 computer processor cores," says University of California, Berkeley graduate student Evangelos Georganas. "With this tool, we estimate that the output from the world's biomedical sequencing capacity could be assembled using just a portion of [the National Energy Research Scientific Computing Center's] Edison supercomputer."
To make efficient use of massively parallel systems, Georganas developed an algorithm for de novo assembly that exploits the one-sided communication and Partitioned Global Address Space (PGAS) capabilities of the UPC programming language. PGAS enables researchers to treat the physically independent memories of each supercomputer node as one address space, reducing the time and energy the supercomputer spends swapping information between nodes.
Lawrence Berkeley National Laboratory Computational Research Division researcher Leonid Oliker says the new parallel algorithms enable the rapid performance of assembly calculations. Meraculous developer Jarrod Chapman thinks this milestone could make metagenome analysis by the tool possible.
From Berkeley Lab News Center
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