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Management of High-Throughput DNA Sequencing Projects: Alpheus

By Neil A. Miller, Andrew Farmer, Stephen F. Kingsmore, Raymond J. Langley, Faye D. Schilkey, Joann Mudge, John A. Crow, Alvaro J. Gonzalez, Ryan J. Kim, Jennifer Van Velkinburgh, Gregory D. May, C. Forrest Black, M. Kathy Myers, John P. Utsey, Nicholas S. Frost and Ernest F. Retzel

Abstract

Copyright: © 2008 Neil AM, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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), Roche-454 (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 is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls based on consistency, expecte

Year: 2008
OAI identifier: oai:CiteSeerX.psu:10.1.1.183.6191
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