PT  - JOURNAL ARTICLE
AU  - Chen-Shan Chin
AU  - Paul Peluso
AU  - Fritz J. Sedlazeck
AU  - Maria Nattestad
AU  - Gregory T. Concepcion
AU  - Alicia Clum
AU  - Christopher Dunn
AU  - Ronan O'Malley
AU  - Rosa Figueroa-Balderas
AU  - Abraham Morales-Cruz
AU  - Grant R. Cramer
AU  - Massimo Delledonne
AU  - Chongyuan Luo
AU  - Joseph R. Ecker
AU  - Dario Cantu
AU  - David R. Rank
AU  - Michael C. Schatz
TI  - Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
AID  - 10.1101/056887
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 056887
4099  - http://biorxiv.org/content/early/2016/06/03/056887.short
4100  - http://biorxiv.org/content/early/2016/06/03/056887.full
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.