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The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

View ORCID ProfileOlga Dudchenko, View ORCID ProfileMuhammad S. Shamim, View ORCID ProfileSanjit S. Batra, Neva C. Durand, Nathaniel T. Musial, Ragib Mostofa, Melanie Pham, Brian Glenn St Hilaire, Weijie Yao, Elena Stamenova, Marie Hoeger, Sarah K. Nyquist, Valeriya Korchina, Kelcie Pletch, Joseph P. Flanagan, Ania Tomaszewicz, Denise McAloose, Cynthia Pérez Estrada, Ben J. Novak, View ORCID ProfileArina D. Omer, View ORCID ProfileErez Lieberman Aiden
doi: https://doi.org/10.1101/254797
Olga Dudchenko
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
4Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA.
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  • ORCID record for Olga Dudchenko
Muhammad S. Shamim
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
5Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA.
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Sanjit S. Batra
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
6Department of Computer Science, University of California, Berkeley, CA 94720, USA.
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Neva C. Durand
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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Nathaniel T. Musial
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
7Erik Jonsson School of Engineering and Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA.
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Ragib Mostofa
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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Melanie Pham
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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Brian Glenn St Hilaire
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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Weijie Yao
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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Elena Stamenova
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
8Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
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Marie Hoeger
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
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Sarah K. Nyquist
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
9Computational and Systems Biology, MIT, Cambridge, MA 02139, USA.
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Valeriya Korchina
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
10DMU College of Osteopathic Medicine, Des Moines University, Des Moines, IA 50312, USA.
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Kelcie Pletch
11Houston Zoo, Houston, TX 77030, USA.
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Joseph P. Flanagan
11Houston Zoo, Houston, TX 77030, USA.
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Ania Tomaszewicz
12Wildlife Conservation Society, New York, NY 10460, USA.
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Denise McAloose
12Wildlife Conservation Society, New York, NY 10460, USA.
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Cynthia Pérez Estrada
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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Ben J. Novak
13Revive and Restore, Sausalito, CA 94965, USA.
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Arina D. Omer
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
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Erez Lieberman Aiden
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
4Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA.
8Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
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  • For correspondence: erez@erez.com
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Article Information

doi 
https://doi.org/10.1101/254797
History 
  • January 28, 2018.
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.

Author Information

  1. Olga Dudchenko1,2,3,4,
  2. Muhammad S. Shamim1,2,3,5,†,
  3. Sanjit S. Batra1,6,†,
  4. Neva C. Durand1,2,3,
  5. Nathaniel T. Musial1,7,
  6. Ragib Mostofa1,3,
  7. Melanie Pham1,2,3,
  8. Brian Glenn St Hilaire1,2,3,
  9. Weijie Yao1,2,3,
  10. Elena Stamenova1,8,
  11. Marie Hoeger1,
  12. Sarah K. Nyquist1,9,
  13. Valeriya Korchina1,10,
  14. Kelcie Pletch11,
  15. Joseph P. Flanagan11,
  16. Ania Tomaszewicz12,
  17. Denise McAloose12,
  18. Cynthia Pérez Estrada1,2,3,
  19. Ben J. Novak13,
  20. Arina D. Omer1,2,3 and
  21. Erez Lieberman Aiden1,2,3,4,8,*
  1. 1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
  2. 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  3. 3Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
  4. 4Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA.
  5. 5Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA.
  6. 6Department of Computer Science, University of California, Berkeley, CA 94720, USA.
  7. 7Erik Jonsson School of Engineering and Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA.
  8. 8Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
  9. 9Computational and Systems Biology, MIT, Cambridge, MA 02139, USA.
  10. 10DMU College of Osteopathic Medicine, Des Moines University, Des Moines, IA 50312, USA.
  11. 11Houston Zoo, Houston, TX 77030, USA.
  12. 12Wildlife Conservation Society, New York, NY 10460, USA.
  13. 13Revive and Restore, Sausalito, CA 94965, USA.
  1. ↵*Correspondence to: erez{at}erez.com.
  1. ↵† These authors contributed equally to this work.

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The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000
Olga Dudchenko, Muhammad S. Shamim, Sanjit S. Batra, Neva C. Durand, Nathaniel T. Musial, Ragib Mostofa, Melanie Pham, Brian Glenn St Hilaire, Weijie Yao, Elena Stamenova, Marie Hoeger, Sarah K. Nyquist, Valeriya Korchina, Kelcie Pletch, Joseph P. Flanagan, Ania Tomaszewicz, Denise McAloose, Cynthia Pérez Estrada, Ben J. Novak, Arina D. Omer, Erez Lieberman Aiden
bioRxiv 254797; doi: https://doi.org/10.1101/254797
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The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000
Olga Dudchenko, Muhammad S. Shamim, Sanjit S. Batra, Neva C. Durand, Nathaniel T. Musial, Ragib Mostofa, Melanie Pham, Brian Glenn St Hilaire, Weijie Yao, Elena Stamenova, Marie Hoeger, Sarah K. Nyquist, Valeriya Korchina, Kelcie Pletch, Joseph P. Flanagan, Ania Tomaszewicz, Denise McAloose, Cynthia Pérez Estrada, Ben J. Novak, Arina D. Omer, Erez Lieberman Aiden
bioRxiv 254797; doi: https://doi.org/10.1101/254797

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