Using optical mapping data for the improvement of vertebrate genome assemblies
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Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science. 1993;262:110–4.
Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol. 2013;31:135–41.
Ananiev GE, Goldstein S, Runnheim R, Forrest DK, Zhou S, Potamousis K, et al. Optical mapping discerns genome wide DNA methylation profiles. BMC Mol Biol. 2008;9:68.
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, et al. Modernizing reference genome assemblies. PLoS Biol. 2011;9:e1001091.
Genome Reference Consortium. http://genomereference.org (2014). Accessed 17 Dec 2014.
Giacalone J, Delobette S, Gibaja V, Ni L, Skiadas Y, Qi R, et al. Optical mapping of BAC clones from the human Y chromosome DAZ locus. Genome Res. 2000;10:1421–9.
Levy-Sakin M, Ebenstein Y. Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy. Curr Opin Biotechnol. 2013;24:690–8.
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008;453:56–64.
Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, et al. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol. 2009;7:e1000112.
Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, et al. High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A. 2010;107:10848–53.
Riley MC, Lee JE, Lesho E, Kirkup Jr BC. Optically mapping multiple bacterial genomes simultaneously in a single run. PLoS One. 2011;6:e27085.
OpGen. http://www.opgen.com (2015). Accessed 17 Dec 2014.
Das SK, Austin MD, Akana MC, Deshpande P, Cao H, Xiao M. Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes. Nucleic Acids Res. 2010;38:e177.
BioNano Genomics. http://www.bionanogenomics.com (2013). Accessed 17 Dec 2014.
Baday M, Cravens A, Hastie A, Kim H, Kudeki DE, Kwok PY, et al. Multicolor super-resolution DNA imaging for genetic analysis. Nano Lett. 2012;12:3861–6.
Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol. 2012;30:771–6.
O'Bleness M, Searles VB, Dickens CM, Astling D, Albracht D, Mak AC, et al. Finished sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome. BMC Genomics. 2014;15:387.
van Heesch S, Kloosterman WP, Lansu N, Ruzius FP, Levandowsky E, Lee CC, et al. Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing. BMC Genomics. 2013;14:257.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013;2:10.
Goldstein S, Schwartz DW. Germinate & Grow: A de Bruijn assembly algorithm for optical maps. F1000Posters. 2011. http://f1000.com/posters/browse/summary/1047 . Accessed 17 Dec 2014.
Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, et al. High-coverage sequencing and annotated assemblies of the budgerigar genome. Gigascience. 2014;3:11.
Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, et al. Using population admixture to help complete maps of the human genome. Nat Genet. 2013;45:406–14.
Genovese G, Handsaker RE, Li H, Kenny EE, McCarroll SA. Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes. Am J Hum Genet. 2013;93:411–21.
Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013;496:498–503.
gEVAL - The Genome Evaluation Browser. http://geval.sanger.ac.uk (2014). Accessed 17 Dec 2014.
Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, Agarwala R, Huddleston J, et al. Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res. 2014;24(12):2066–76.