DeeZ: reference-based compression by local assembly

Article metrics

Access 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

    Hach, F., Numanagic, I., Alkan, C. & Sahinalp, S.C. Bioinformatics 28, 3051–3057 (2012).

  2. 2

    Kozanitis, C., Saunders, C., Kruglyak, S., Bafna, V. & Varghese, G. J. Comput. Biol. 18, 401–413 (2011).

  3. 3

    Cox, A.J., Bauer, M.J., Jakobi, T. & Rosone, G. Bioinformatics 28, 1415–1419 (2012).

  4. 4

    Deorowicz, S. & Grabowski, S. Bioinformatics 27, 860–862 (2011).

  5. 5

    Jones, D.C., Ruzzo, W.L., Peng, X. & Katze, M.G. Nucleic Acids Res. 40, e171 (2012).

  6. 6

    Bonfield, J.K. & Mahoney, M.V. PLoS ONE 8, e59190 (2013).

  7. 7

    Bonfield, J.K. Bioinformatics 30, 2818–2819 (2014).

  8. 8

    Li, H. et al. Bioinformatics 25, 2078–2079 (2009).

Download references

Acknowledgements

We thank the Natural Sciences and Engineering Research Council of Canada (NSERC) for the Discovery Frontiers “Cancer Genome Collaboratory” project, Discovery Grants program and Genome Canada (S.C.S.) and the Vanier Canada Graduate Scholarship program (I.N.) for funding this research. We also thank L. Stein, T. Beck and H. Babaran as well as L. Ding and R.J. Mashi for testing and benchmarking the performance of DeeZ. We thank J. Bonfield for helping us to improve DeeZ. We thank J. Dale, G. Asimenos and S. Batzoglou for support in the initial stages of this research.

Author information

Correspondence to S Cenk Sahinalp.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text

Supplementary Note (PDF 407 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Hach, F., Numanagic, I. & Sahinalp, S. DeeZ: reference-based compression by local assembly. Nat Methods 11, 1082–1084 (2014) doi:10.1038/nmeth.3133

Download citation

Further reading