All 17 genomes were assembled with the VGP pipeline (Extended Data Fig. 2a) for benchmark purposes, with some uncurated. The pale spear-nosed bat, greater horseshoe bat, Canada lynx, platypus, male and female zebra finch, kākāpō, Anna’s hummingbird, Goode’s thornscrub tortoise, flier cichlid, and blunt-snouted clingfish assemblies were generated using the VGP pipeline 1.0 to 1.6 and curated for submission to NCBI and EBI public archives. The curated and submitted two-lined caecilian, zig-zag eel, climbing perch, channel bull blenny, eastern happy, and thorny skate assemblies were generated using a similar process developed in parallel (Supplementary Note 2). Two submitted curated versions of the female zebra finch were made, one using the standard VGP pipeline and the other using the VGP trio pipeline, so that comparative analyses could be performed by others.
Rhie A., McCarthy S.A., Fedrigo O., Damas J., Formenti G., Koren S., Uliano-Silva M., Chow W., Fungtammasan A., Kim J., Lee C., Ko B.J., Chaisson M., Gedman G.L., Cantin L.J., Thibaud-Nissen F., Haggerty L., Bista I., Smith M., Haase B., Mountcastle J., Winkler S., Paez S., Howard J., Vernes S.C., Lama T.M., Grutzner F., Warren W.C., Balakrishnan C.N., Burt D., George J.M., Biegler M.T., Iorns D., Digby A., Eason D., Robertson B., Edwards T., Wilkinson M., Turner G., Meyer A., Kautt A.F., Franchini P., Detrich HW I.I.I., Svardal H., Wagner M., Naylor G.J., Pippel M., Malinsky M., Mooney M., Simbirsky M., Hannigan B.T., Pesout T., Houck M., Misuraca A., Kingan S.B., Hall R., Kronenberg Z., Sović I., Dunn C., Ning Z., Hastie A., Lee J., Selvaraj S., Green R.E., Putnam N.H., Gut I., Ghurye J., Garrison E., Sims Y., Collins J., Pelan S., Torrance J., Tracey A., Wood J., Dagnew R.E., Guan D., London S.E., Clayton D.F., Mello C.V., Friedrich S.R., Lovell P.V., Osipova E., Al-Ajli F.O., Secomandi S., Kim H., Theofanopoulou C., Hiller M., Zhou Y., Harris R.S., Makova K.D., Medvedev P., Hoffman J., Masterson P., Clark K., Martin F., Howe K., Flicek P., Walenz B.P., Kwak W., Clawson H., Diekhans M., Nassar L., Paten B., Kraus R.H., Crawford A.J., Gilbert M.T., Zhang G., Venkatesh B., Murphy R.W., Koepfli K.P., Shapiro B., Johnson W.E., Di Palma F., Marques-Bonet T., Teeling E.C., Warnow T., Graves J.M., Ryder O.A., Haussler D., O’Brien S.J., Korlach J., Lewin H.A., Howe K., Myers E.W., Durbin R., Phillippy A.M, & Jarvis E.D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737-746.
Other organizations :
National Human Genome Research Institute, National Institutes of Health, University of Cambridge, Rockefeller University, University of California, Davis, Leibniz Institute for Zoo and Wildlife Research, Wellcome Sanger Institute, DNAnexus (United States), Seoul National University, University of Southern California, National Center for Biotechnology Information, European Bioinformatics Institute, Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Institute for Psycholinguistics, University of Massachusetts Amherst, University of Adelaide, University of Missouri, East Carolina University, University of Queensland, Clemson University, University of Otago, University of Arizona, Natural History Museum, Bangor University, University of Konstanz, NOAA National Marine Fisheries Service Northeast Fisheries Science Center, Northeastern University, University of Antwerp, University of Graz, University of Florida, Florida Museum of Natural History, Technology Affinity Group, University of California, Santa Cruz, San Diego Zoo Institute for Conservation Research, Zoological Society of San Diego, Pacific Biosciences (United States), BioNano Genomics (United States), Arima Genomics (United States), Santa Cruz County Office of Education, Centre for Genomic Regulation, Dovetail Genomics (United States), Harbin Institute of Technology, University of Chicago, Oregon Health & Science University, Center for Systems Biology Dresden, Monash University Malaysia, University of Milan, LOEWE Centre for Translational Biodiversity Genomics, BGI Group (China), Pennsylvania State University, Universidad de Los Andes, University of Copenhagen, China National GeneBank, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Royal Ontario Museum, Smithsonian Conservation Biology Institute, National Zoological Park, University of East Anglia, Earlham Institute, Institut de Biologia Evolutiva, University College Dublin, University of Illinois Urbana-Champaign, La Trobe University, ITMO University, Howard Hughes Medical Institute
Pipeline version (VGP pipeline 1.0 to 1.6, similar process developed in parallel)
dependent variables
Genome assembly quality
control variables
Benchmark purposes
Curation status (curated vs. uncurated)
controls
The curated and submitted two-lined caecilian, zig-zag eel, climbing perch, channel bull blenny, eastern happy, and thorny skate assemblies were generated using a similar process developed in parallel (Supplementary Note 2).
Two submitted curated versions of the female zebra finch were made, one using the standard VGP pipeline and the other using the VGP trio pipeline, so that comparative analyses could be performed by others.
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