RT Journal Article SR Electronic T1 Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes JF bioRxiv FD Cold Spring Harbor Laboratory SP 064352 DO 10.1101/064352 A1 Derek M. Bickhart A1 Benjamin D. Rosen A1 Sergey Koren A1 Brian L. Sayre A1 Alex R. Hastie A1 Saki Chan A1 Joyce Lee A1 Ernest T. Lam A1 Ivan Liachko A1 Shawn T. Sullivan A1 Joshua N. Burton A1 Heather J. Huson A1 Christy M. Kelley A1 Jana L. Hutchison A1 Yang Zhou A1 Jiajie Sun A1 Alessandra Crisà A1 F. Abel Ponce De León A1 John C. Schwartz A1 John A. Hammond A1 Geoffrey C. Waldbieser A1 Steven G. Schroeder A1 George E. Liu A1 Maitreya J. Dunham A1 Jay Shendure A1 Tad S. Sonstegard A1 Adam M. Phillippy A1 Curtis P. Van Tassell A1 Timothy P.L. Smith YR 2016 UL http://biorxiv.org/content/early/2016/07/18/064352.abstract AB The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.