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

Delphine Larivière^#¹, Linelle Abueg^#², Nadolina Brajuka^#², Cristóbal Gallardo-Alba³, Bjorn Grüning³, Byung June Ko⁴, Alex Ostrovsky⁵, Marc Palmada-Flores⁶, Brandon D Pickett⁷, Keon Rabbani⁸, Agostinho Antunes^{9

10}, Jennifer R Balacco², Mark J P Chaisson⁸, Haoyu Cheng^{11

12}, Joanna Collins¹³, Melanie Couture², Alexandra Denisova¹⁴, Olivier Fedrigo², Guido Roberto Gallo¹⁵, Alice Maria Giani¹⁶, Grenville MacDonald Gooder², Kathleen Horan², Nivesh Jain², Cassidy Johnson², Heebal Kim^{4

17

18}, Chul Lee^{18

19}, Tomas Marques-Bonet^{6

20

21

22}, Brian O'Toole², Arang Rhie⁷, Simona Secomandi²³, Marcella Sozzoni²⁴, Tatiana Tilley², Marcela Uliano-Silva²⁵, Marius van den Beek¹, Robert W Williams²⁶, Robert M Waterhouse²⁷, Adam M Phillippy⁷, Erich D Jarvis²⁸, Michael C Schatz²⁹, Anton Nekrutenko³⁰, Giulio Formenti³¹

Affiliations

¹ Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
² Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
³ Bioinformatics Group, Department of Computer Science, Albert-Ludwigs University Freiburg, Freiburg, Germany.
⁴ Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
⁵ Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁶ Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain.
⁷ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
⁸ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
⁹ CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
¹⁰ Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
¹¹ Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
¹² Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹³ Wellcome Sanger Institute, Cambridge, UK.
¹⁴ Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
¹⁵ Department of Biosciences, University of Milan, Milan, Italy.
¹⁶ BMRI, Weill Cornell Medical College, New York, NY, USA.
¹⁷ eGnome, Inc., Seoul, Republic of Korea.
¹⁸ Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
¹⁹ Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
²⁰ Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.
²¹ CNAG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
²² Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
²³ Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
²⁴ University of Florence, Department of Biology, Florence, Italy.
²⁵ Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
²⁶ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
²⁷ Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
²⁸ Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA. ejarvis@rockefeller.edu.
²⁹ Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA. mschatz@cs.jhu.edu.
³⁰ Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. anton@nekrut.org.
³¹ Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA. gformenti@rockefeller.edu.

^# Contributed equally.

PMID: 38278971
PMCID: PMC11462542
DOI: 10.1038/s41587-023-02100-3

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

Delphine Larivière et al. Nat Biotechnol. 2024 Mar.

. 2024 Mar;42(3):367-370.

doi: 10.1038/s41587-023-02100-3.

Authors

Affiliations

¹ Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
² Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
³ Bioinformatics Group, Department of Computer Science, Albert-Ludwigs University Freiburg, Freiburg, Germany.
⁴ Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
⁵ Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁶ Department of Medicine and Life Sciences (MELIS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain.
⁷ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
⁸ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
⁹ CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
¹⁰ Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
¹¹ Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
¹² Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹³ Wellcome Sanger Institute, Cambridge, UK.
¹⁴ Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
¹⁵ Department of Biosciences, University of Milan, Milan, Italy.
¹⁶ BMRI, Weill Cornell Medical College, New York, NY, USA.
¹⁷ eGnome, Inc., Seoul, Republic of Korea.
¹⁸ Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
¹⁹ Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
²⁰ Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.
²¹ CNAG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
²² Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
²³ Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
²⁴ University of Florence, Department of Biology, Florence, Italy.
²⁵ Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
²⁶ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
²⁷ Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
²⁸ Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA. ejarvis@rockefeller.edu.
²⁹ Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA. mschatz@cs.jhu.edu.
³⁰ Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. anton@nekrut.org.
³¹ Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA. gformenti@rockefeller.edu.

^# Contributed equally.

PMID: 38278971
PMCID: PMC11462542
DOI: 10.1038/s41587-023-02100-3

No abstract available

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Conflict of interest statement

Competing interests

The authors declare no competing interests.

Figures

**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.**
A decision on whether to invoke workflow 6 is based on the analysis of QC output of workflows 3, 4 or 5 (see Supplementary Information for full explanation). Thicker lines connecting workflows 7, 8 and 9 reflect the fact that these workflows are invoked separately for each phased assembly (once for maternal and once for paternal).

**Fig. 2 |. Phylogenetic tree and assembly statistics of genomes assembled using the VGP–Galaxy assembly pipeline.**
From the innermost circle to the outermost circle: (i) repeat content; (ii) heterozygosity; (iii) heterogamy: individuals with two identical sex chromosomes (white) or two different sex chromosomes (blue); (iv) assembly size in percentage of the genome size estimated by Genomescope; (v) scaffold NG50 in % of estimated genome size; (vi) Merqury completeness of both haplotypes; (vii) BUSCO completeness: presence of orthologous genes present and complete compared to the set expected in vertebrates; (viii) mitogenome assembled and available (black); (ix) genome size in gigabytes, with lines at 9, 2, 3, 4, 6 and 8 Gb; (x) number of scaffolds in log scale, with lines at 1 (10 scaffolds), 2 (100 scaffolds), 3 (1,000 scaffolds) and 4 (10,000 scaffolds).

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Update of

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.
Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. Larivière D, et al. bioRxiv [Preprint]. 2023 Jun 30:2023.06.28.546576. doi: 10.1101/2023.06.28.546576. bioRxiv. 2023. Update in: Nat Biotechnol. 2024 Mar;42(3):367-370. doi: 10.1038/s41587-023-02100-3. PMID: 37425881 Free PMC article. Updated. Preprint.

References

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1. Formenti G et al. Trends Ecol. Evol. 37, 197–202 (2022). - PubMed
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1. Rhie A, Walenz BP, Koren S & Phillippy AM Genome Biol. 21, 245 (2020). - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Conflict of interest statement

Figures

Update of

References

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MeSH terms

Grants and funding

LinkOut - more resources

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