Outside of the simplest cases (haploid, bacteria, or inbreds), genomic information is not carried in a single reference per individual, but rather has higher ploidy (n=>2) for almost all organisms. The existence of two or more highly related sequences within an individual makes it extremely difficult to build high quality, highly contiguous genome assemblies from short DNA fragments. Based on the earlier work on a polyploidy aware assembler, FALCON ( https://github.com/PacificBiosciences/FALCON) , we developed new algorithms and software (“FALCON-unzip”) for de novo haplotype reconstructions from SMRT Sequencing data. We generate two datasets for developing the algorithms and the prototype software:…
In recent years, human genomic research has focused on comparing short-read data sets to a single human reference genome. However, it is becoming increasingly clear that significant structural variations present in individual human genomes are missed or ignored by this approach. Additionally, remapping short-read data limits the phasing of variation among individual chromosomes. This reduces the newly sequenced genome to a table of single nucleotide polymorphisms (SNPs) with little to no information as to the co-linearity (phasing) of these variants, resulting in a “mosaic” reference representing neither of the parental chromosomes. The variation between the homologous chromosomes is lost in…
A high quality reference genome is an essential resource for plant and animal breeding and functional and evolutionary studies. The common hop (Humulus lupulus, Cannabaceae) is an economically important crop plant used to flavor and preserve beer. Its genome is large (flow cytometrybased estimates of diploid length >5.4Gb1), highly repetitive, and individual plants display high levels of heterozygosity, which make assembly of an accurate and contiguous reference genome challenging with conventional short-read methods. We present a contig assembly of Cascade Hops using PacBio long reads and the diploid genome assembler, FALCON-Unzip2. The assembly has dramatically improved contiguity and completeness over…