@article{87d60ed05a374d7482522f4309d7180f,
title = "Assembly and diploid architecture of an individual human genome via single-molecule technologies",
abstract = "We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.",
author = "Matthew Pendleton and Robert Sebra and Pang, {Andy Wing Chun} and Ajay Ummat and Oscar Franzen and Tobias Rausch and St{\"u}tz, {Adrian M.} and William Stedman and Thomas Anantharaman and Alex Hastie and Heng Dai and Fritz, {Markus Hsi Yang} and Han Cao and Ariella Cohain and Gintaras Deikus and Durrett, {Russell E.} and Blanchard, {Scott C.} and Roger Altman and Chin, {Chen Shan} and Yan Guo and Paxinos, {Ellen E.} and Korbel, {Jan O.} and Darnell, {Robert B.} and McCombie, {W. Richard} and Kwok, {Pui Yan} and Mason, {Christopher E.} and Schadt, {Eric E.} and Ali Bashir",
note = "Funding Information: R01 DK098242-01, R01 MH106531, US National Institutes of Health (NIH) U41HG007497, the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, the STARR Consortium, the WorldQuant Foundation, the Pershing Square Foundation, the Genomics & Epigenomics Core Facilities and SMRT Sequencing Center at Weill Cornell Medical College, and through the computational resources and staff expertise provided by the Department of Scientific Computing at the Icahn School of Medicine at Mount Sinai. DNA samples were provided by the Coriell Institute for Medical Research and the US National Institute of Standards and Technology (NIST). We would also like to thank T. Zichner for assistance with the design of validations and M. Chaisson for assistance with running Blasr, the assembly-based SV pipeline, and in performing the CHM1 comparison. Funding Information: This work was supported in part by institutional support from the Icahn Institute for Genomics and Multiscale Biology, R01 HG005946, U01 HL107388, Publisher Copyright: {\textcopyright} 2015 Nature America, Inc. All rights reserved.",
year = "2015",
month = jul,
day = "30",
doi = "10.1038/nmeth.3454",
language = "English",
volume = "12",
pages = "780--786",
journal = "Nature Methods",
issn = "1548-7091",
publisher = "Nature Publishing Group",
number = "8",
}