RT Journal Article
SR Electronic
T1 Single-molecule sequencing and conformational capture enable <em>de novo</em> mammalian reference genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 064352
DO 10.1101/064352
A1 Bickhart, Derek M.
A1 Rosen, Benjamin D.
A1 Koren, Sergey
A1 Sayre, Brian L.
A1 Hastie, Alex R.
A1 Chan, Saki
A1 Lee, Joyce
A1 Lam, Ernest T.
A1 Liachko, Ivan
A1 Sullivan, Shawn T.
A1 Burton, Joshua N.
A1 Huson, Heather J.
A1 Kelley, Christy M.
A1 Hutchison, Jana L.
A1 Zhou, Yang
A1 Sun, Jiajie
A1 Crisà, Alessandra
A1 De León, F. Abel Ponce
A1 Schwartz, John C.
A1 Hammond, John A.
A1 Waldbieser, Geoffrey C.
A1 Schroeder, Steven G.
A1 Liu, George E.
A1 Dunham, Maitreya J.
A1 Shendure, Jay
A1 Sonstegard, Tad S.
A1 Phillippy, Adam M.
A1 Van Tassell, Curtis P.
A1 Smith, Timothy P.L.
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 &gt;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.