Publication: Modernizing reference genome assemblies

PubMed ID: 21750661

Citation: Church DM, Schneider VA, Graves T, et al. Modernizing reference genome assemblies. PLoS Biol. 2011;9(7):e1001091. doi:10.1371/journal.pbio.1001091

Funding: The GRC would like to acknowledge the following contributors to this project: David C. Schwartz, Jane Rogers, Mario Caccamo, Paul Kitts, Michael DiCuccio, Françoise Thibaud-Nissen, Avi Kimchi, Jonathan Mudge, Richard Clark, Andrew Dearlove, Michelle Smitth, Britt Kilian, Karen McLaren, James Gilbert, Laurens Wilming, Darren Ware, Sharmin Begum, Karen Davey, Diana Kidger, Kim Brugger, Tony Gaige, and Jason Walker.

Publication: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

PubMed ID: 28396521

Citation: Schneider VA, Graves-Lindsay T, Howe K, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 2017;27(5):849-864. doi:10.1101/gr.213611.116

Funding: This research was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine, the Wellcome Trust (grant numbers WT095908, WT098051, and WT104947/Z/14/Z), and the European Molecular Biology Laboratory. S.K. and A.M.P. were supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health. This study utilized the computational resources of the Biowulf system at the National Institutes of Health, Bethesda, MD (http://biowulf.nih.gov). Work at MGI was supported by National Institutes of Health grants 5U54HG003079 and 5U41HG007635. Work by E.E.E. was supported in part by National Institutes of Health grants HG002385 and HG007635. E.E.E. is an investigator of the Howard Hughes Medical Institute. The GRC wishes to acknowledge the invaluable assistance and contributions of the many external collaborators and the RefSeq and HAVANA annotation groups who shared data, expertise, and advice in the effort to update the reference assembly sequence. A list of genome-wide and region-specific collaborators can be found at the GRC website (https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/credits.shtml). Additionally, the GRC would like to thank Jim Knight and Stephan Schuster for submitting sequence from an RP11-based WGS assembly to INSDC (GCA_000442295.1), making it available for use in reference curation. The MGI would like to thank Susie Rock and Aye Wollam for their oversight of the assembly curation and finishing pipelines at the McDonnell Genome Institute. WTSI thanks Paul Heath, Guy Griffiths, Britt Killian, and Eduardus Zuiderwijk for their technical and computational contributions. NCBI thanks Tayebeh Rezaie-Jami, Eugene Yaschenko, Avi Kimchi, and Karen Clark for their helpful discussion and expertise in content and data management, and Chris O'Sullivan for providing the SRA and dbGaP submission statistics. EBI thanks Bronwen Aken for providing the ENA submission statistics, as well as Carlos García Girón and Amonida Zadissa. We thank Uravashi Surti for her work to develop the CHM1 and CHM13 cell lines.