Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
Larivière, Delphine (Pennsylvania State University)
Abueg, Linelle Ann L. (The Rockefeller University)
Brajuka, Nadolina (The Rockefeller University)
Gallardo, Cristobal (Albert-Ludwigs-University Freiburg)
Grüning, Björn (Albert-Ludwigs-University Freiburg)
Ko, Byung June (Seoul National University)
Ostrovsky, Alexander (Johns Hopkins University)
Palmada-Flores, Marc (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Pickett, Brandon (National Institutes of Health. National Human Genome Research Institute (USA))
Rabbani, Keon (University of Southern California)
Balacco, Jennifer (The Rockefeller University)
Chaisson, Mark (University of Southern California)
Cheng, Haoyu (Harvard Medical School)
Collins, Joanna (Wellcome Sanger Institute (Regne Unit))
Denisova, Alexandra (Lomonosov Moscow State University)
Fedrigo, Olivier (The Rockefeller University)
Gallo, Guido (Università degli Studi di Milano)
Giani, Alice Maria (Weill Cornell Medical College (USA))
Gooder, Grenville MacDonald (The Rockefeller University)
Jain, Nivesh (The Rockefeller University)
Johnson, Cassidy (The Rockefeller University)
Kim, Heebal (Seoul National University)
Lee, Chul (The Rockefeller University)
Marques-Bonet, Tomas 1975- (Institut Català de Paleontologia Miquel Crusafont)
O'Toole, Brian (The Rockefeller University)
Rhie, Arang (National Institutes of Health. National Human Genome Research Institute (USA))
Secomandi, Simona (University of Cyprus)
Sozzoni, Marcella (Università di Firenze)
Tilley, Tatiana (The Rockefeller University)
Uliano da Silva, Marcela (Wellcome Sanger Institute (Regne Unit))
van den Beek, Marius (Pennsylvania State University)
Waterhouse, Robert (University of Lausanne)
Phillippy, Adam M. (National Institutes of Health. National Human Genome Research Institute (USA))
Jarvis, Erich (The Rockefeller University)
Schatz, Michael (Johns Hopkins University)
Nekrutenko, Anton (Pennsylvania State University)
Formenti, Giulio (The Rockefeller University)

Data:	2024
Resum:	Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).
Ajuts:	European Commission 101059492
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.
Llengua:	Anglès
Document:	Prepublicació ; recerca ; Versió de l'autor
Matèria:	Genome assembly ; Opensource ; Large genomes ; Public ; Scalable ; Accessible ; Modularity ; Reproducibility
Obra relacionada:	Larivière, D., Abueg, L., Brajuka, N. et al. "Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy". Nature Biotechnology. Vol. 42, (March 2024), p. 367-370 https://doi.org/10.1038/s41587-023-02100-3

DOI: 10.1101/2023.06.28.546576
PMID: 37425881

29 p, 2.9 MB

El registre apareix a les col·leccions:
Documents de recerca > Documents dels grups de recerca de la UAB > Centres i grups de recerca (producció científica) > Ciències > Institut Català de Paleontologia Miquel Crusafont (ICP)
Documents de recerca > Prepublicacions