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Mind the gaps

Nature Methods volume 7, pages 105–106 (2010)Cite this article

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By grouping short reads derived from the same long genomic fragment, the reads can easily be assembled into fragments that approach the length of capillary sequencing reads.

Amid all the excitement about next-generation sequencing, scientists often neglect to mention the problems that are caused by short read lengths. Genome assemblies produced from short reads are far more fragmented than those produced from long reads, with many more gaps and with relatively poor long-range linking information. Fortunately, technology to produce long reads is still being pursued vigorously in some laboratories. In this issue, a group led by Jay Shendure1 describes a method to create 'reads' as long as 700 base pairs (bp) starting with pairs of reads that are just 20 bp and 76 bp.

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Figure 1: Turning short reads into long reads using subassembly.

References

  1. Hiatt, J.B., Patwardhan, R.P., Turner, E.H., Lee, C. & Shendure, J. Nat. Methods 7, 119–122 (2010).

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Authors and Affiliations

  1. Steven L. Salzberg is at the Center for Bioinformatics and Computational Biology and Department of Computer Science, University of Maryland, College Park, Maryland, USA. salzberg@umd.edu,

    Steven L Salzberg

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  1. Steven L Salzberg
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Salzberg, S. Mind the gaps. Nat Methods 7, 105–106 (2010). https://doi.org/10.1038/nmeth0210-105

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  • DOI: https://doi.org/10.1038/nmeth0210-105

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