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Visualizing genomes: techniques and challenges

Nature Methods volume 7, pages S5–S15 (2010)Cite this article

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Abstract

As our ability to generate sequencing data continues to increase, data analysis is replacing data generation as the rate-limiting step in genomics studies. Here we provide a guide to genomic data visualization tools that facilitate analysis tasks by enabling researchers to explore, interpret and manipulate their data, and in some cases perform on-the-fly computations. We will discuss graphical methods designed for the analysis of de novo sequencing assemblies and read alignments, genome browsing, and comparative genomics, highlighting the strengths and limitations of these approaches and the challenges ahead.

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Figure 1: Screenshots of connected views in Consed.
Figure 2: The UCSC Genome and Cancer Genomics Browsers.
Figure 3: The VISTA browser.

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Acknowledgements

Thanks to Y. Butterfield, S. Diguistini, P. Gorniak, M. Krzywinski, N. Liao, G. Robertson and G. Taylor for helpful discussions and comments. C.B.N. was funded with US federal funds from the National Cancer Institute, National Institutes of Health (NIH), under contract no. NO1-CO-12400. The contributions of M.C. and I.D. were performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Livermore National Laboratory under contract no. DE-AC52-07NA27344, Lawrence Berkeley National Laboratory under contract no. DE-AC02-05CH11231, and Los Alamos National Laboratory under contract no. DE-AC02-06NA25396. D.G. was supported by NIH grants R01 HL094976 and 1RC2HL10296-01 and by the Howard Hughes Medical Institute. T.W. was supported by funds from the Helen Hay Whitney Foundation.

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Authors and Affiliations

  1. British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia, Canada

    Cydney B Nielsen

  2. Department of Energy Joint Genome Institutes, Walnut Creek, California, USA

    Michael Cantor & Inna Dubchak

  3. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Inna Dubchak

  4. Department of Genome Sciences, University of Washington, Seattle, Washington, USA

    David Gordon

  5. Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri, USA

    Ting Wang

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  1. Cydney B Nielsen
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Correspondence to Cydney B Nielsen.

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Nielsen, C., Cantor, M., Dubchak, I. et al. Visualizing genomes: techniques and challenges. Nat Methods 7 (Suppl 3), S5–S15 (2010). https://doi.org/10.1038/nmeth.1422

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