Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms (original) (raw)

References

  1. Soneson, C. & Delorenzi, M. BMC Bioinformatics 14, 91 (2013).
    Article Google Scholar
  2. Roychowdhury, S. et al. Sci. Trans. Med. 111ra121 (2011).
  3. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Genome Biol. 10, R25 (2009).
    Article Google Scholar
  4. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Nat. Methods 5, 621–628 (2008).
    Article CAS Google Scholar
  5. Trapnell, C. et al. Nat. Biotechnol. 28, 511–515 (2010).
    Article CAS Google Scholar
  6. Li, B. & Dewey, C. BMC Bioinformatics 12, 323 (2011).
    Article CAS Google Scholar
  7. Roberts, A. & Pachter, L. Nat. Methods 10, 71–73 (2012).
    Article Google Scholar
  8. Philippe, N., Salson, M., Commes, T. & Rivals, E. Genome Biol. 14, R30 (2013).
    Article Google Scholar
  9. Botelho, F.C., Pagh, R. & Ziviani, N. Proceedings of the 10th International Workshop on Algorithms and Data Structures Halifax, NS, Canada, August 15–17, 2007 (eds. Dehne, F., Sack, J.-R. & Zeh, N.)139–150 (Springer, 2007).
  10. Marçais, G. & Kingsford, C. Bioinformatics 27, 764–770 (2011).
    Article Google Scholar
  11. Varadhan, R. & Roland, C. Scand. J. Stat. 35, 335–353 (2008).
    Article Google Scholar
  12. Nicolae, M., Mangul, S., Mandoiu, I. & Zelikovsky, A. Algorithms Mol. Biol. 6, 9 (2011).
    Article Google Scholar
  13. Salzman, J., Jiang, H. & Wong, W.H. Stat. Sci. 26, 62–83 (2011).
    Article Google Scholar
  14. Zheng, W., Chung, L.M. & Zhao, H. BMC Bioinformatics 12, 290 (2011).
    Article CAS Google Scholar
  15. Shi, L. et al. Nat. Biotechnol. 24, 1151–1161 (2006).
    Article CAS Google Scholar
  16. Bullard, J.H., Purdom, E., Hansen, K.D. & Dudoit, S. BMC Bioinformatics 11, 94 (2010).
    Article Google Scholar
  17. Griebel, T. et al. Nucleic Acids Res. 40, 10073–10083 (2012).
    Article CAS Google Scholar
  18. Grabherr, M.G. et al. Nat. Biotechnol. 29, 644–652 (2011).
    Article CAS Google Scholar
  19. Sacomoto, G.A. et al. BMC Bioinformatics 13 (suppl. 6), S5 (2012).
    PubMed PubMed Central Google Scholar
  20. Pruitt, K.D., Tatusova, T., Brown, G.R. & Maglott, D.R. Nucleic Acids Res. 40, D1, D130–D135 (2012).
    Article Google Scholar
  21. Flicek, P. et al. Nucleic Acids Res. 41, D1, D48–D55 (2013).
    Google Scholar
  22. Trapnell, C., Pachter, L. & Salzberg, S. Bioinformatics 25, 1105–1111 (2009).
    Article CAS Google Scholar
  23. Pheatt, C. J. Comput. Sci. Coll. 23, 298–298 (2008).
    Google Scholar

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