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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

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Fig. 1: VGP–Galaxy assembly pipeline (version 2.1) consists of 10 workflows that can be combined into 8 analysis trajectories depending on the combination of input data.
Fig. 2: Phylogenetic tree and assembly statistics of genomes assembled using the VGP–Galaxy assembly pipeline.

Data availability

The workflows, their description and instructions on how to use them can be found at https://galaxyproject.org/projects/vgp/workflows/. The requisite tools are installed on usegalaxy.org and usegalaxy.eu, and are in the process of being installed on usegalaxy.org.au. These genomes were supported by collaborators of the VGP and ERGA, and the QC analyses reported here to test the VGP Galaxy pipeline do not release those that are under specific embargo policies for genome-wide analyses (e.g., https://genome10k.ucsc.edu/data-use-policies/). New genome assemblies are available in the GenomeArk repository: https://www.genomeark.org/. After manual curation, the assemblies are submitted to the US National Center for Biotechnology Information (NCBI) under the BioProject Vertebrate Genome Project: https://www.ncbi.nlm.nih.gov/bioproject/48924317.

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Author information

Author notes

  1. These authors contributed equally: Delphine Larivière, Linelle Abueg, Nadolina Brajuka

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA

    Delphine Larivière, Marius van den Beek & Anton Nekrutenko

  2. Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA

    Linelle Abueg, Nadolina Brajuka, Jennifer R. Balacco, Melanie Couture, Olivier Fedrigo, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Brian O’Toole, Tatiana Tilley, Erich D. Jarvis & Giulio Formenti

  3. Bioinformatics Group, Department of Computer Science, Albert-Ludwigs University Freiburg, Freiburg, Germany

    Cristóbal Gallardo-Alba & Bjorn Grüning

  4. Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea

    Byung June Ko & Heebal Kim

  5. Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA

    Alex Ostrovsky & Michael C. Schatz

  6. Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain

    Marc Palmada-Flores & Tomas Marques-Bonet

  7. Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

    Brandon D. Pickett, Arang Rhie & Adam M. Phillippy

  8. Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA

    Keon Rabbani & Mark J. P. Chaisson

  9. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal

    Agostinho Antunes

  10. Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal

    Agostinho Antunes

  11. Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA

    Haoyu Cheng

  12. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

    Haoyu Cheng

  13. Wellcome Sanger Institute, Cambridge, UK

    Joanna Collins

  14. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia

    Alexandra Denisova

  15. Department of Biosciences, University of Milan, Milan, Italy

    Guido Roberto Gallo

  16. BMRI, Weill Cornell Medical College, New York, NY, USA

    Alice Maria Giani

  17. eGnome, Inc., Seoul, Republic of Korea

    Heebal Kim

  18. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea

    Heebal Kim & Chul Lee

  19. Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA

    Chul Lee

  20. Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain

    Tomas Marques-Bonet

  21. CNAG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

    Tomas Marques-Bonet

  22. Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain

    Tomas Marques-Bonet

  23. Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus

    Simona Secomandi

  24. University of Florence, Department of Biology, Florence, Italy

    Marcella Sozzoni

  25. Tree of Life, Wellcome Sanger Institute, Cambridge, UK

    Marcela Uliano-Silva

  26. Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA

    Robert W. Williams

  27. Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland

    Robert M. Waterhouse

Authors
  1. Delphine Larivière
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  2. Linelle Abueg
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  3. Nadolina Brajuka
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  4. Cristóbal Gallardo-Alba
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  5. Bjorn Grüning
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  6. Byung June Ko
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  7. Alex Ostrovsky
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  8. Marc Palmada-Flores
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  9. Brandon D. Pickett
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  10. Keon Rabbani
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  11. Agostinho Antunes
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  14. Haoyu Cheng
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  15. Joanna Collins
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  16. Melanie Couture
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  17. Alexandra Denisova
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  18. Olivier Fedrigo
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  19. Guido Roberto Gallo
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  20. Alice Maria Giani
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  21. Grenville MacDonald Gooder
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  22. Kathleen Horan
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  23. Nivesh Jain
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  24. Cassidy Johnson
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  26. Chul Lee
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  28. Brian O’Toole
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  29. Arang Rhie
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  32. Tatiana Tilley
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  33. Marcela Uliano-Silva
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  34. Marius van den Beek
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  35. Robert W. Williams
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  36. Robert M. Waterhouse
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  37. Adam M. Phillippy
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  38. Erich D. Jarvis
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  39. Michael C. Schatz
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  40. Anton Nekrutenko
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  41. Giulio Formenti
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Contributions

D.L. built the assembly pipeline with support from G.F., L.A., C.G.-A., B.G., A.O., H.C., M.U.-S., B.D.P., A.R., M.v.d.B. and the VGP assembly working group. L.A., A.D., G.R.G., A.M.G., G.M.G., N.J., C.J., B.O., S.S., M.S. and T.T. generated one or several assemblies used in the analyses. B.J.K., K.R. and M.J.P.C. validated the zebra finch assemblies. J.C. performed the manual curation on the zebra finch assembly. L.A. assembled and evaluated the mitochondrial genomes. N.B. established the decontamination pipeline and performed the contamination analyses. N.B. and M.P.-F. compared the scaffolding strategies. A.N. performed the analyses on XBP1. C.G.-A. and B.D.P. developed the training material with support from the user community. K.H. and M.C. sourced and arranged for sample procurement for species in this study. J.R.B., N.J., T.T., B.O’T., O.F., C.L., H.K., T.M.-B. and R.M.W. generated the PacBio and Hi-C data. G.F., M.C.S., A.N., A.M.P. and E.D.J. conceived the study and drafted the manuscript. All authors, including A.A. and R.W.W., contributed to writing and editing the manuscript and approved it.

Corresponding authors

Correspondence to Erich D. Jarvis, Michael C. Schatz, Anton Nekrutenko or Giulio Formenti.

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Competing interests

The authors declare no competing interests.

Supplementary information

Supplementary Information

Supplementary Notes and Supplementary Figs. 1–14

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Supplementary Tables 1–10

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Larivière, D., Abueg, L., Brajuka, N. et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol 42, 367–370 (2024). https://doi.org/10.1038/s41587-023-02100-3

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