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Parallel, tag-directed assembly of locally derived short sequence reads

Nature Methods volume 7, pages 119–122 (2010)Cite this article

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Abstract

We demonstrate subassembly, an in vitro library construction method that extends the utility of short-read sequencing platforms to applications requiring long, accurate reads. A long DNA fragment library is converted to a population of nested sublibraries, and a tag sequence directs grouping of short reads derived from the same long fragment, enabling localized assembly of long fragment sequences. Subassembly may facilitate accurate de novo genome assembly and metagenome sequencing.

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Figure 1: Schematic of subassembly process.
Figure 2: Evaluation of subassembly performance.

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Acknowledgements

We thank L. Chistoserdova and M.G. Kalyuzhnaya (University of Washington) for the gift of the methylamine-enriched metagenomic DNA sample, C. Manoil (University of Washington) for the gift of P. aeruginosa strain PAO1 genomic DNA and P. Green for helpful discussions. J.B.H. is supported by US National Institutes of Health grant T32GM007266 and an Achievement Rewards for College Scientists fellowship.

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Author notes

  1. Joseph B Hiatt and Rupali P Patwardhan: These authors contributed equally to this work.

Authors and Affiliations

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

    Joseph B Hiatt, Rupali P Patwardhan, Emily H Turner, Choli Lee & Jay Shendure

Authors
  1. Joseph B Hiatt
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  2. Rupali P Patwardhan
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  3. Emily H Turner
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  4. Choli Lee
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  5. Jay Shendure
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Contributions

E.H.T. and J.S. conceived the initial approach. All authors contributed to subsequent experimental design. J.B.H. and E.H.T. developed library construction methods. C.L. performed Illumina sequencing. R.P.P. developed the subassembly computational pipeline and iterative scaffolding algorithm. J.B.H., R.P.P. and J.S. analyzed data. All authors contributed to writing of the manuscript. J.S. supervised all aspects of the study.

Corresponding authors

Correspondence to Joseph B Hiatt or Jay Shendure.

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Competing interests

J.S., J.B.H., R.P.P. and E.H.T. are authors of a patent application for the method described in this paper (US Provisional Application number 61/096,720).

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Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Tables 1–4, Supplementary Notes 1–4 and Supplementary Protocols 1–3 (PDF 837 kb)

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Hiatt, J., Patwardhan, R., Turner, E. et al. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods 7, 119–122 (2010). https://doi.org/10.1038/nmeth.1416

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