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Cloud computing tools and analyses

The next generation sequencing 'problem', namely the generation of huge datasets that are unwieldy for analyses and expensive and problematic to store, has been remedied by the advent of cloud computing, where one rents hardware or storage space. This phenomenon has revolutionized genomic analyses and brought large-scale genomics within reach of smaller labs. The following Genome Biology articles showcase tools and examples of studies that use such technologies.

  1. Research

    Sequencing and analysis of an Irish human genome

    Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci. Here, choosing a DNA sample from a pop...

    Pin Tong, James GD Prendergast, Amanda J Lohan, Susan M Farrington, Simon Cronin, Nial Friel, Dan G Bradley, Orla Hardiman, Alex Evans, James F Wilson and Brendan Loftus

    Genome Biology 2010 11:R91

    Published on: 7 September 2010

  2. Software

    Cloud-scale RNA-sequencing differential expression analysis with Myrna

    As sequencing throughput approaches dozens of gigabases per day, there is a growing need for efficient software for analysis of transcriptome sequencing (RNA-Seq) data. Myrna is a cloud-computing pipeline for ...

    Ben Langmead, Kasper D Hansen and Jeffrey T Leek

    Genome Biology 2010 11:R83

    Published on: 11 August 2010

  3. Correspondence

    Translational bioinformatics in the cloud: an affordable alternative

    With the continued exponential expansion of publicly available genomic data and access to low-cost, high-throughput molecular technologies for profiling patient populations, computational technologies and info...

    Joel T Dudley, Yannick Pouliot, Rong Chen, Alexander A Morgan and Atul J Butte

    Genome Medicine 2010 2:51

    Published on: 6 August 2010

  4. Methodology article

    Cloud computing for comparative genomics

    Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastruct...

    Dennis P Wall, Parul Kudtarkar, Vincent A Fusaro, Rimma Pivovarov, Prasad Patil and Peter J Tonellato

    BMC Bioinformatics 2010 11:259

    Published on: 18 May 2010

  5. Software

    Searching for SNPs with cloud computing

    As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bow...

    Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop and Steven L Salzberg

    Genome Biology 2009 10:R134

    Published on: 20 November 2009