PT  - JOURNAL ARTICLE
AU  - Derek M. Bickhart
AU  - Benjamin D. Rosen
AU  - Sergey Koren
AU  - Brian L. Sayre
AU  - Alex R. Hastie
AU  - Saki Chan
AU  - Joyce Lee
AU  - Ernest T. Lam
AU  - Ivan Liachko
AU  - Shawn T. Sullivan
AU  - Joshua N. Burton
AU  - Heather J. Huson
AU  - Christy M. Kelley
AU  - Jana L. Hutchison
AU  - Yang Zhou
AU  - Jiajie Sun
AU  - Alessandra Crisà
AU  - F. Abel Ponce De León
AU  - John C. Schwartz
AU  - John A. Hammond
AU  - Geoffrey C. Waldbieser
AU  - Steven G. Schroeder
AU  - George E. Liu
AU  - Maitreya J. Dunham
AU  - Jay Shendure
AU  - Tad S. Sonstegard
AU  - Adam M. Phillippy
AU  - Curtis P. Van Tassell
AU  - Timothy P.L. Smith
TI  - Single-molecule sequencing and conformational capture enable <em>de novo</em> mammalian reference genomes
AID  - 10.1101/064352
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 064352
4099  - http://biorxiv.org/content/early/2016/07/18/064352.short
4100  - http://biorxiv.org/content/early/2016/07/18/064352.full
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.