Larivière, Delphine, Abueg, Linelle, Brajuka, Nadolina, Gallardo-Alba, Cristóbal, Grüning, Bjorn, Ko, Byung June, Ostrovsky, Alex, Palmada-Flores, Marc, Pickett, Brandon D, Rabbani, Keon, Balacco, Jennifer R, Chaisson, Mark, Cheng, Haoyu, Collins, Joanna, Denisova, Alexandra, Fedrigo, Olivier, Gallo, Guido Roberto, Giani, Alice Maria, Gooder, Grenville MacDonald, Jain, Nivesh, Johnson, Cassidy, Kim, Heebal, Lee, Chul, Marques-Bonet, Tomas, O'Toole, Brian, Rhie, Arang, Secomandi, Simona, Sozzoni, Marcella, Tilley, Tatiana, Uliano-Silva, Marcela, van den Beek, Marius, Waterhouse, Robert M, Phillippy, Adam M, Jarvis, Erich D, Schatz, Michael C, Nekrutenko, Anton, Formenti, Giulio (June 2023) Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. (Submitted)
Preview |
PDF
2023_Lariviere_Scalable_Accessible_and_Reproducible_Reference_Genome.pdf - Submitted Version Available under License Creative Commons Attribution. Download (3MB) | Preview |
Abstract
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).
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > analysis and processing > reference assembly |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 30 June 2023 |
| Date Deposited: | 21 Sep 2023 20:27 |
| Last Modified: | 21 Sep 2023 20:27 |
| PMCID: | PMC10327048 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/40961 |
Actions (login required)
 |
Administrator's edit/view item |