Test driving genome assemblers

Two head-to-head comparisons of genome assembly methods highlight the best performers and outstanding problems.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Generating a genome sequence by next-generation sequencing and de novo assembly.

References

  1. 1

    Salzberg, S.L. et al. Genome Res. 22, 557–567 (2012).

  2. 2

    Earl, D. et al. Genome Res. 21, 2224–2241 (2011).

  3. 3

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

  4. 4

    Gnerre, S. et al. Proc. Natl. Acad. Sci. USA 108, 1513–1518 (2011).

  5. 5

    Koren, S., Treangen, T.J. & Pop, M. Bioinformatics 27, 2964–2971 (2011).

  6. 6

    Miller, J.R. et al. Bioinformatics 24, 2818–2824 (2008).

  7. 7

    Simpson, J.T. & Durbin, R. Genome Res. 22, 549–556 (2012).

  8. 8

    Li, R. et al. Genome Res. 20, 265–272 (2010).

  9. 9

    Zerbino, D.R. & Birney, E. Genome Res. 18, 821–829 (2008).

  10. 10

    Li, R. et al. Nature 463, 311–317 (2010).

  11. 11

    Alkan, C., Sajjadian, S. & Eichler, E.E. Nat. Methods 8, 61–65 (2011).

  12. 12

    Iqbal, Z., Caccamo, M., Turner, I., Flicek, P. & McVean, G. Nat. Genet. 44, 226–232 (2012).

Download references

Author information

Correspondence to Ruiqiang Li.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Fan, W., Li, R. Test driving genome assemblers. Nat Biotechnol 30, 330–331 (2012). https://doi.org/10.1038/nbt.2172

Download citation

Further reading