RT Journal Article
SR Electronic
T1 Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 056887
DO 10.1101/056887
A1 Chen-Shan Chin
A1 Paul Peluso
A1 Fritz J. Sedlazeck
A1 Maria Nattestad
A1 Gregory T. Concepcion
A1 Alicia Clum
A1 Christopher Dunn
A1 Ronan O'Malley
A1 Rosa Figueroa-Balderas
A1 Abraham Morales-Cruz
A1 Grant R. Cramer
A1 Massimo Delledonne
A1 Chongyuan Luo
A1 Joseph R. Ecker
A1 Dario Cantu
A1 David R. Rank
A1 Michael C. Schatz
YR 2016
UL http://biorxiv.org/content/early/2016/06/03/056887.abstract
AB While genome assembly projects have been successful in a number of haploid or inbred species, one of the current main challenges is assembling non-inbred or rearranged heterozygous genomes. To address this critical need, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble Single Molecule Real-Time (SMRT®) Sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We demonstrate the quality of this approach by assembling new reference sequences for three heterozygous samples, including an F1 hybrid of the model species Arabidopsis thaliana, the widely cultivated V. vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata that have challenged short-read assembly approaches. The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches. The phased diploid assembly enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.