June 1, 2021

Data release for polymorphic genome assembly algorithm development.

Author(s): Badgett, Marty R. and Chin, Jason and Rank, David and Peluso, Paul and Karalius, Joseph and Bernal, Maria and Krämer, Ute and Kim, Sangtae and Lanz, Christa and Weigel, Detlef and Luo, Chongyuan and O’Malley, Ronan and Ecker, Joe

Heterozygous and highly polymorphic diploid (2n) and higher polyploidy (n > 2) genomes have proven to be very difficult to assemble. One key to the successful assembly and phasing of polymorphic genomics is the very long read length (9-40 kb) provided by the PacBio RS II system. We recently released software and methods that facilitate the assembly and phasing of genomes with ploidy levels equal to or greater than 2n. In an effort to collaborate and spur on algorithm development for assembly and phasing of heterozygous polymorphic genomes, we have recently released sequencing datasets that can be used to test and develop highly polymorphic diploid and polyploidy assembly and phasing algorithms. These data sets include multiple species and ecotypes of Arabidopsis that can be combined to create synthetic in-silico F1 hybrids with varying levels of heterozygosity. Because the sequence of each individual line was generated independently, the data set provides a ‘ground truth’ answer for the expected results allowing the evaluation of assembly algorithms. The sequencing data, assembly of inbred and in-silico heterozygous samples (n=>2) and phasing statistics will be presented. The raw and processed data has been made available to aid other groups in the development of phasing and assembly algorithms.

Organization: PacBio
Year: 2014

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