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Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

View ORCID ProfileJoel Armstrong, Glenn Hickey, View ORCID ProfileMark Diekhans, Alden Deran, Qi Fang, Duo Xie, Shaohong Feng, Josefin Stiller, Diane Genereux, Jeremy Johnson, Voichita Dana Marinescu, David Haussler, Jessica Alföldi, Kerstin Lindblad-Toh, Elinor Karlsson, Guojie Zhang, Benedict Paten
doi: https://doi.org/10.1101/730531
Joel Armstrong
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, USA
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  • ORCID record for Joel Armstrong
Glenn Hickey
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, USA
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Mark Diekhans
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, USA
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Alden Deran
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, USA
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Qi Fang
2China National GeneBank, BGI–Shenzhen, Shenzhen 518083, China
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Duo Xie
2China National GeneBank, BGI–Shenzhen, Shenzhen 518083, China
3University of Chinese Academy of Sciences, Beijing 100049, China
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Shaohong Feng
2China National GeneBank, BGI–Shenzhen, Shenzhen 518083, China
4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Josefin Stiller
5Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
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Diane Genereux
6Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Jeremy Johnson
6Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Voichita Dana Marinescu
7Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
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David Haussler
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, USA
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Jessica Alföldi
6Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Kerstin Lindblad-Toh
6Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
7Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
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Elinor Karlsson
6Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
8Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
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Guojie Zhang
2China National GeneBank, BGI–Shenzhen, Shenzhen 518083, China
4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
5Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
9Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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Benedict Paten
1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, USA
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  • For correspondence: bpaten@ucsc.edu
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Article Information

doi 
https://doi.org/10.1101/730531
History 
  • August 9, 2019.

Article Versions

  • You are currently viewing Version 1 of this article (August 9, 2019 - 09:56).
  • Version 2 (August 26, 2019 - 01:38).
  • View Version 3, the most recent version of this article.
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-ND 4.0 International license.

Author Information

  1. Joel Armstrong1,
  2. Glenn Hickey1,
  3. Mark Diekhans1,
  4. Alden Deran1,
  5. Qi Fang2,
  6. Duo Xie2,3,
  7. Shaohong Feng2,4,
  8. Josefin Stiller5,
  9. Diane Genereux6,
  10. Jeremy Johnson6,
  11. Voichita Dana Marinescu7,
  12. David Haussler1,
  13. Jessica Alföldi6,
  14. Kerstin Lindblad-Toh6,7,
  15. Elinor Karlsson6,8,
  16. Guojie Zhang2,4,5,9 and
  17. Benedict Paten*,1
  1. 1UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA 95060, USA
  2. 2China National GeneBank, BGI–Shenzhen, Shenzhen 518083, China
  3. 3University of Chinese Academy of Sciences, Beijing 100049, China
  4. 4State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
  5. 5Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
  6. 6Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
  7. 7Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
  8. 8Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
  9. 9Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
  1. ↵*Corresponding author. Email: bpaten{at}ucsc.edu
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Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era
Joel Armstrong, Glenn Hickey, Mark Diekhans, Alden Deran, Qi Fang, Duo Xie, Shaohong Feng, Josefin Stiller, Diane Genereux, Jeremy Johnson, Voichita Dana Marinescu, David Haussler, Jessica Alföldi, Kerstin Lindblad-Toh, Elinor Karlsson, Guojie Zhang, Benedict Paten
bioRxiv 730531; doi: https://doi.org/10.1101/730531
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Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era
Joel Armstrong, Glenn Hickey, Mark Diekhans, Alden Deran, Qi Fang, Duo Xie, Shaohong Feng, Josefin Stiller, Diane Genereux, Jeremy Johnson, Voichita Dana Marinescu, David Haussler, Jessica Alföldi, Kerstin Lindblad-Toh, Elinor Karlsson, Guojie Zhang, Benedict Paten
bioRxiv 730531; doi: https://doi.org/10.1101/730531

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