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Management of High-Throughput DNA Sequencing Projects: Alpheus

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Author(s): Neil A. Miller | Stephen F. Kingsmore | Andrew D.Farmer | Raymond J. Langley | Joann Mudge

Journal: Journal of Computer Science & Systems Biology
ISSN 0974-7230

Volume: 01;
Issue: 01;
Start page: 132;
Date: 2008;
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Keywords: Alpheus | sequencing-by-synthesis | pyrosequencing | GMAP | GSNAP | resequencing | transcriptome sequencing

ABSTRACT
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 inter-related 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), Roche-454 (pyrosequencing) and Applied Biosystem’s SOLiD (sequencing-by-ligation). Alpheus enables alignmentto reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. Alpheus is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stopcodons, and splice isoforms. Variant detection is aided by the ability to filter variant calls dynamically based on consistency,expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. Alpheus also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.
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