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A Python-based programming language for high-performance computational genomics

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Fig. 1: The Seq programming language.


  1. Yu, Y. W., Daniels, N. M., Danko, D. C. & Berger, B. Cell Syst. 1, 130–140 (2015).

    CAS  Article  Google Scholar 

  2. Peng, R. D. Science 334, 1226–1227 (2011).

    CAS  Article  Google Scholar 

  3. Baker, M. Nature 533, 452–454 (2016).

    CAS  Article  Google Scholar 

  4. Lee, R. S. & Hanage, W. P. Lancet Microbe (2020).

  5. Perkel, J. M. Nature 588, 185–186 (2020).

    CAS  Article  Google Scholar 

  6. Köster, J. Bioinformatics 32, 444–446 (2016).

    Article  Google Scholar 

  7. Döring, A., Weese, D., Rausch, T. & Reinert, K. BMC Bioinformatics 9, 11 (2008).

    Article  Google Scholar 

  8. Reinert, K. et al. J. Biotechnol. 261, 157–168 (2017).

    CAS  Article  Google Scholar 

  9. Ward, B. J. BioJulia (accessed 19 November 2020).

  10. Cock, P. J. et al. Bioinformatics 25, 1422–1423 (2009).

    CAS  Article  Google Scholar 

  11. Russell, P. H., Johnson, R. L., Ananthan, S., Harnke, B. & Carlson, N. E. PLoS One 13, e0205898 (2018).

    Article  Google Scholar 

  12. Stajich, J. E. et al. Genome Res. 12, 1611–1618 (2002).

    CAS  Article  Google Scholar 

  13. Li, H. Preprint at (2013).

  14. Yorukoglu, D., Yu, Y. W., Peng, J. & Berger, B. Nat. Biotechnol. 34, 374–376 (2016).

    CAS  Article  Google Scholar 

  15. Hach, F. et al. Nucleic Acids Res. 42, W494–W500 (2014).

    CAS  Article  Google Scholar 

  16. Li, H. Bioinformatics 34, 3094–3100 (2018).

    CAS  Article  Google Scholar 

  17. Smith, T., Heger, A. & Sudbery, I. Genome Res. 27, 491–499 (2017).

    CAS  Article  Google Scholar 

  18. McKenna, A. et al. Genome Res. 20, 1297–1303 (2010).

    CAS  Article  Google Scholar 

  19. Bray, N., Dubchak, I. & Pachter, L. Genome Res. 13, 97–102 (2003).

    CAS  Article  Google Scholar 

  20. Berger, E. et al. Nat. Commun. 11, 4662 (2020).

    CAS  Article  Google Scholar 

  21. Berger, E., Yorukoglu, D. & Berger, B. International Conference on Research in Computational Molecular Biology 28–29 (Springer, 2015).

  22. Abelson, H. & Sussman, G. J. Structure and Interpretation of Computer Programs (MIT Press, 1996).

  23. Shajii, A., Numanagić, I., Baghdadi, R., Berger, B. & Amarasinghe, S. Proc. ACM Program. Lang. 3, 125:1–125:29 (2019).

    Article  Google Scholar 

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Correspondence to Saman Amarasinghe or Bonnie Berger.

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Peer review information Nature Biotechnology thanks Ivan Costa and Judith Zaugg for their contribution to the peer review of this work.

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Supplementary Notes 1–4, including Figs. 1–5 and Tables 1–8

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Shajii, A., Numanagić, I., Leighton, A.T. et al. A Python-based programming language for high-performance computational genomics. Nat Biotechnol 39, 1062–1064 (2021).

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