Rapid advances in high-throughput sequencers have made it possible to obtain large amounts of whole genome data quickly and inexpensively. As the amount of data increases, the increase in computation time has become a...
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Rapid advances in high-throughput sequencers have made it possible to obtain large amounts of whole genome data quickly and inexpensively. As the amount of data increases, the increase in computation time has become a...
Rapid advances in high-throughput sequencers have made it possible to obtain large amounts of whole genome data quickly and inexpensively. As the amount of data increases, the increase in computation time has become a serious problem. One of the main causes of this problem is file I/O performance. Most pipelines do not implement file I/O suitable for distributed file systems, which are common storage systems in parallel computers used for large-scale analysis. In this study, we developed an I/O system adapted to distributed file systems. In the proposed system, storage access frequency was suppres.ed by I/O buffers, and thread parallelization by OpenMP was employed. We tested the developed system and a high parallel speedup was achieved. Availability: The developed system is freely available from https://***/SatoshiITO/GAPS
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