2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2018

Chen-Shan Chin, Paul Peluso, Fritz J. Sedlazeck, Maria Nattestad, Gregory T. Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R. Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R. Ecker, Dario Cantu, David R. Rank, Michael C. Schatz. Phased diploid genome assembly with single-molecule real-time sequencing. Nature methods, 13(12):1050-1054. 2016.

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While genome assembly projects have been successful in many haploid and inbred
species, the assembly of noninbred or rearranged heterozygous genomes remains a
major challenge. To address this challenge, we introduce the open-source FALCON
and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to
assemble long-read sequencing data into highly accurate, contiguous, and
correctly phased diploid genomes. We generate new reference sequences for
heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely
cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus
Clavicorona pyxidata, samples that have challenged short-read assembly
approaches. The FALCON-based assemblies are substantially more contiguous and
complete than alternate short- or long-read approaches. The phased diploid
assembly enabled the study of haplotype structure and heterozygosities between
homologous chromosomes, including the identification of widespread heterozygous
structural variation within coding sequences.