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Full-Text Articles in Computer Engineering
Scalable Data Structure To Compress Next-Generation Sequencing Files And Its Application To Compressive Genomics, Sandino Vargas-Perez, Fahad Saeed
Scalable Data Structure To Compress Next-Generation Sequencing Files And Its Application To Compressive Genomics, Sandino Vargas-Perez, Fahad Saeed
Parallel Computing and Data Science Lab Technical Reports
It is now possible to compress and decompress large-scale Next-Generation Sequencing files taking advantage of high-performance computing techniques. To this end, we have recently introduced a scalable hybrid parallel algorithm, called phyNGSC, which allows fast compression as well as decompression of big FASTQ datasets using distributed and shared memory programming models via MPI and OpenMP. In this paper we present the design and implementation of a novel parallel data structure which lessens the dependency on decompression and facilitates the handling of DNA sequences in their compressed state using fine-grained decompression in a technique that is identified as in …
Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed
Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed
Parallel Computing and Data Science Lab Technical Reports
Proteogenomics is an emerging field of systems biology research at the intersection of proteomics and genomics. Two high-throughput technologies, Mass Spectrometry (MS) for proteomics and Next Generation Sequencing (NGS) machines for genomics are required to conduct proteogenomics studies. Independently both MS and NGS technologies are inflicted with data deluge which creates problems of storage, transfer, analysis and visualization. Integrating these big data sets (NGS+MS) for proteogenomics studies compounds all of the associated computational problems. Existing sequential algorithms for these proteogenomics datasets analysis are inadequate for big data and high performance computing (HPC) solutions are almost non-existent. The purpose of this …
A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed
A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed
Parallel Computing and Data Science Lab Technical Reports
With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results show …