Journal of Management of High-Throughput DNA Sequencing Projects: Alpheus
High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and interrelated data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multigigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche454 (pyrosequencing) and Applied Biosystem’s SOLiD (sequencing-by-ligation). Alpheus enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence.
Alpheus was designed with an underlying relational database management system. The current installation is on Sybase 12.5.4. We are, however, presently developing toward an implementation on the Kognitio’s (Berkshire, UK & Chicago, IL, USA) WX2 analytical database. The WX2 database has the advantage of rapid loading of large tables, as well as a parallel implementation both for loading and
querying. Because of the underlying massively parallel hardware configuration, WX2 significantly reduces many common data management tasks.
Download Journal pdf:
http://alpheus.ncgr.org/pubs/JCSB1.132.pdf
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