Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Delphine Larivière, Marius van den Beek and Anton Nekrutenko
Vertebrate Genome Laboratory, Rockefeller University, New York, NY, USA.
Linelle Abueg, Nadolina Brajuka, Jennifer R. Balacco, Melanie Couture, Oliver Fedrigo, Grenville MacDonald Gooder, Kathleen Horan, Nivesh Jain, Cassidy Johnson, Brian O’Toole, Tatiana Tilley, Erich D. Jarvis and Giulio Formenti
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
Cristóbal Gallardo-Alba & Bjorn Grüning
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
Byung June Ko and Heebal Kim
Departments of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Alex Ostrovsky and Michael C. Schatz
Department of Medicine and Life Sciences (MELIS), Institute of Evolutionary Biology, Pompeu Fabra University-CSIC, Barcelona, Spain
Marc Palmada-Flores & Tomas Marques-Bonet
Genome Informatics Section, Statistical and Computational Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Brandon D. Pickett, Arang Rhie and Adam M. Phillippy
Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Keon Rabbani and Mark J.P. Chaisson
CIIMAR/CIMAR, Interdisciplinary Center for Marine and Environmental Research, University of Porto, Porto, Portugal
Agustín Antunes
Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
Agustín Antunes
Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Hao Yu Cheng
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Hao Yu Cheng
Wellcome Sanger Institute, Cambridge, United Kingdom
Joanna Collins
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
Alexandra Denisova
Department of Biosciences, University of Milan, Milan, Italy
Guido Roberto Gallo
BMRI, Weill Cornell Medical College, New York, NY, USA.
Alicia Maria Giani
eGnome, Inc., Seoul, Republic of Korea
Heebal Kim
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
Heebal Kim and Chul Lee
Language Neurogenetics Laboratory, Rockefeller University, New York, NY, USA.
Chul Lee
Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
Tomas Marques-Bonet
CNAG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
Tomas Marques-Bonet
Miquel Crusafont Catalan Institute of Paleontology, Autonomous University of Barcelona, Cerdanyola del Vallès, Spain
Tomas Marques-Bonet
Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
Simona Secomandi
University of Florence, Department of Biology, Florence, Italy
Marcella Sozzoni
Tree of Life, Wellcome Sanger Institute, Cambridge, UK
Marcela Uliano-Silva
Department of Genetics, Genomics, and Informatics, University of Tennessee Health Sciences Center, Memphis, TN, USA.
Robert Williams
Department of Ecology and Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
Robert M. Waterhouse
DL built the assembly process with the support of GF, LA, CG-A., BG, AO, HC, MU-S., BDP, AR, MvdB and the VGP assembly working group. LA, AD, GRG, AMG, GMG, NJ, CJ, BO, SS, MS, and TT generated one or more sets used in the analyses. BJK, KR, and MJPC validated the zebra finch assemblies. JC performed manual healing of the zebra finch assembly. LA assembled and evaluated the mitochondrial genomes. NB established the decontamination pipeline and performed contamination analyses. NB and MP-F. compared scaffolding strategies. AN performed the analyzes in XBP1. CG-A. and BDP developed the training material with the support of the user community. KH and MC obtained and organized sample acquisition for the species in this study. JRB, New Jersey, T.T., B.O’T., OF, CL, HK, TM-B. and RMW generated the PacBio and Hi-C data. GF, MCS, AN, AMP, and EDJ conceived the study and wrote the manuscript. All authors, including AA and RWW, contributed to the writing and editing of the manuscript and approved it.
