Brief Communication | Published:

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

Nature Methods volume 7, pages 119122 (2010) | Download Citation

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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    & Nat. Biotechnol. 26, 1135–1145 (2008).

  2. 2.

    et al. Nat. Methods 5, 183–188 (2008).

  3. 3.

    , , , & Nat. Methods 5, 621–628 (2008).

  4. 4.

    & Genome Res. 19, 1141–1152 (2009).

  5. 5.

    et al. Genome Res. 19, 1117–1123 (2009).

  6. 6.

    , , , & Science 324, 807–810 (2009).

  7. 7.

    et al. Tissue Antigens 74, 393–403 (2009).

  8. 8.

    et al. Nature 437, 376–380 (2005).

  9. 9.

    et al. Nat. Biotechnol. 26, 1029–1034 (2008).

  10. 10.

    & Genome Res. 8, 186–194 (1998).

  11. 11.

    et al. Nature 406, 959–964 (2000).

  12. 12.

    et al. Nucleic Acids Res. 25, 3389–3402 (1997).

  13. 13.

    et al. Science 287, 2196–2204 (2000).

  14. 14.

    et al. Genome Res. 19, 294–305 (2009).

  15. 15.

    & Genome Res. 18, 821–829 (2008).

  16. 16.

    & Nat. Methods 6, 673–676 (2009).

  17. 17.

    , , , & Nucleic Acids Res. 27, 4636–4641 (1999).

  18. 18.

    , , & Genome Biol. 10, R25 (2009).

Download references

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.

Author information

Author notes

    • Joseph B Hiatt
    •  & Rupali P Patwardhan

    These authors contributed equally to this work.

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. Search for Joseph B Hiatt in:

  2. Search for Rupali P Patwardhan in:

  3. Search for Emily H Turner in:

  4. Search for Choli Lee in:

  5. Search for Jay Shendure in:

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.

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).

Corresponding authors

Correspondence to Joseph B Hiatt or Jay Shendure.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6, Supplementary Tables 1–4, Supplementary Notes 1–4 and Supplementary Protocols 1–3

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nmeth.1416

Further reading