Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Autor: Pardo-Palacios FJ; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.; These authors contributed equally to this work., Wang D; Department of Biomedical Informatics, The Ohio State University, Columbus, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.; These authors contributed equally to this work., Reese F; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.; These authors contributed equally to this work., Diekhans M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Carbonell-Sala S; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.; These authors contributed equally to this work., Williams B; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.; These authors contributed equally to this work., Loveland JE; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.; These authors contributed equally to this work., De María M; Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.; Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA.; These authors contributed equally to this work., Adams MS; Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Balderrama-Gutierrez G; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.; These authors contributed equally to this work., Behera AK; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Gonzalez JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.; These authors contributed equally to this work., Hunt T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.; These authors contributed equally to this work., Lagarde J; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.; Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain.; These authors contributed equally to this work., Liang CE; Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Li H; Department of Biomedical Informatics, The Ohio State University, Columbus, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.; These authors contributed equally to this work., Jerryd Meade M; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.; These authors contributed equally to this work., Moraga Amador DA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA.; These authors contributed equally to this work., Prjibelski AD; Department of Computer Science, University of Helsinki, Helsinki, Finland.; Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.; These authors contributed equally to this work., Birol I; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Bostan H; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA., Brooks AM; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA., Hasan Çelik M; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Chen Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Du MRM; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia., Felton C; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Göke J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.; Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore., Hafezqorani S; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Herwig R; Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany., Kawaji H; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan., Lee J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Liang Li J; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA., Lienhard M; Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany., Mikheenko A; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK., Mulligan D; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Ming Nip K; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Pertea M; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, USA., Ritchie ME; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.; Department of Medical Biology, The University of Melbourne, Parkville, Australia., Sim AD; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Tang AD; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Kei Wan Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.; Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore., Wang C; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia., Wong BY; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, USA., Yang C; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Barnes I; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Berry A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Capella S; Barcelona Supercomputing Cente, Barcelona, Spain., Dhillon N; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Fernandez-Gonzalez JM; Barcelona Supercomputing Cente, Barcelona, Spain., Ferrández-Peral L; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Garcia-Reyero N; Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA., Goetz S; Biobam Bioinformatics SL, Valencia, Spain., Hernández-Ferrer C; Barcelona Supercomputing Cente, Barcelona, Spain., Kondratova L; Genetics Institute, University of Florida, Gainesville, USA., Liu T; Cardiff University, Cardiff, UK., Martinez-Martin A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Menor C; Biobam Bioinformatics SL, Valencia, Spain., Mestre-Tomás J; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Mudge JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Panayotova NG; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA., Paniagua A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Repchevsky D; Barcelona Supercomputing Cente, Barcelona, Spain., Rouchka E; Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA., Saint-John B; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Sapena E; European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK., Sheynkman L; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA., Laird Smith M; Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA., Suner MM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Takahashi H; Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan., Youngworth IA; Department of Genetics, Stanford University, Palo Alto, USA., Carninci P; Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.; Human Technopole, Milano, Italy., Denslow ND; Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.; Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA., Guigó R; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain., Hunter ME; U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA., Tilgner HU; Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA., Wold BJ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Vollmers C; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Frankish A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Fai Au K; Department of Biomedical Informatics, The Ohio State University, Columbus, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA., Sheynkman GM; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.; Center for Public Health Genomics.; UVA Cancer Center, University of Virginia, Charlottesville, USA., Mortazavi A; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Conesa A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.; Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA., Brooks AN; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2023 Jul 27. Date of Electronic Publication: 2023 Jul 27.