Search Results for "parallel computing"

...It uses the following techniques in order to improve scalability: 1) a fast splitting of the input reads using the FUSE kernel module available in most of current Linux distributions; 2) a balanced on-demand distribution of the reads based on the shared locks of UPC++, an extension of C++ for parallel computing that follows the Partitioned Global Address Space (PGAS) paradigm. parSRA is portable as its configuration file allows the users to parallelize the execution of existing SRA tools without the need to modify the source code of parSRA or the aligner.

Ezys is a non-linear 3D medical image registration program. Ezys fully exploits the parallel computing power of inexpensive commercial graphics processing units (GPU), resulting in a very fast and accurate program capable of running on desktop PCs and even some laptops. On these systems, non-linear image registrations take less than a minute to complete. Ezys implements a diffeomorphic inverse consistent image registration algorithm with a demons-style regularization based on a non-parametric free form deformation model. ...

High-throughput next generation sequencing (NGS) technology has quickly emerged as a powerful tool in many aspects of biomedical research. However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive parallel processing (MPP) systems.

PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. ...