Searching for SNPs with cloud computing
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* Corresponding author: Ben Langmead blangmea@jhsph.edu
Genome Biology 2009, 10:R134 doi:10.1186/gb-2009-10-11-r134
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BioMed Central: 9 citations
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Software
Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke BMC Bioinformatics 2011, 12:356 (30 August 2011) Cloud Virtual Resource (CloVR) is a new desktop application for large-scale sequence analysis using remote computing resources that provides several automated pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis.
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Opinion
The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
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Software
Applications of the pipeline environment for visual informatics and genomics computations Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman, Arthur W Toga BMC Bioinformatics 2011, 12:304 (26 July 2011) |
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Technical Note
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping Tung Nguyen, Weisong Shi, Douglas Ruden BMC Research Notes 2011, 4:171 (6 June 2011) |
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Proceedings
Galaxy CloudMan: delivering cloud compute clusters Enis Afgan, Dannon Baker, Nate Coraor, Brad Chapman, Anton Nekrutenko, James Taylor BMC Bioinformatics 2010, 11(Suppl 12):S4 (21 December 2010) |
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Proceedings
SeqWare Query Engine: storing and searching sequence data in the cloud Brian D O’Connor, Barry Merriman, Stanley F Nelson BMC Bioinformatics 2010, 11(Suppl 12):S2 (21 December 2010) |
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Proceedings
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics Ronald C Taylor BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010) |
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Software
Cloud-scale RNA-sequencing differential expression analysis with Myrna Ben Langmead, Kasper D Hansen, Jeffrey T Leek Genome Biology 2010, 11:R83 (11 August 2010) This article is part of a collection on Cloud computing tools and... Myrna is a software pipeline for calculating differential gene expression from large RNA-seq data sets in the cloud.
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Methodology article
Cloud computing for comparative genomics Dennis P Wall, Parul Kudtarkar, Vincent A Fusaro, Rimma Pivovarov, Prasad Patil, Peter J Tonellato BMC Bioinformatics 2010, 11:259 (18 May 2010) This article is part of a collection on Cloud computing tools and... |