@article {Bickhart064352, author = {Derek M. Bickhart and Benjamin D. Rosen and Sergey Koren and Brian L. Sayre and Alex R. Hastie and Saki Chan and Joyce Lee and Ernest T. Lam and Ivan Liachko and Shawn T. Sullivan and Joshua N. Burton and Heather J. Huson and Christy M. Kelley and Jana L. Hutchison and Yang Zhou and Jiajie Sun and Alessandra Cris{\`a} and F. Abel Ponce De Le{\'o}n and John C. Schwartz and John A. Hammond and Geoffrey C. Waldbieser and Steven G. Schroeder and George E. Liu and Maitreya J. Dunham and Jay Shendure and Tad S. Sonstegard and Adam M. Phillippy and Curtis P. Van Tassell and Timothy P.L. Smith}, title = {Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes}, elocation-id = {064352}, year = {2016}, doi = {10.1101/064352}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2016/07/18/064352}, eprint = {https://www.biorxiv.org/content/early/2016/07/18/064352.full.pdf}, journal = {bioRxiv} }