Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domesticationDomestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala)...
Sun2020 苹果 Phased 2倍体基因组 Sun X, Jiao C, Schwaninger H, et al. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nature Genetics, 2020, DOI: 10.1038/s41588-020-00723-9. 科学网—重磅推荐!康奈尔大学费章君团队揭示苹果驯化...
The open-source FALCON and FALCON-Unzip software utilize long-read sequencing data to generate contiguous, accurate and phased diploid assemblies, even from genomes that are highly heterozygous. While genome assembly projects have been successful in many
FALCON-Phase was developed to solve the problem of haplotype switching in diploid genome assemblies. It has been tested on mammalian assemblies and performs well on an F1 bull with0.7% heterozygosity. It has not been thoroughly tested on samples with very low or very high heterozygosity. In prin...
With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references,...
diploid individual, we introduce the concept of genome heterozygosity by sequence length (GHSL). This approach complements existing k-mer-based methods by quantifying the total sequence length of non-redundant variants (SNPs, indels and SVs) between two haplotypes in phased diploid assemblies (...
config.json: Points to the reference genome and can be used to set optional parameters. assemblies.tsv: A table of input assemblies. Base config: config.json A JSON configuration file,config.json, configures PAV. Default options are built-in, and the only required option isreferencepointing to...
Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner Cet al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.Nat Methods2013;10: 563–569. ArticleCASGoogle Scholar Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock Set al. Gen...
of them 1–9 collapse different homolo-gous haplotypes into a consensus representation with heterozygous alleles frequently switching in the consensus. This approach works well for inbred samples that are nearly homozygous but necessar-ily misses half of the genetic information in a diploid genome. ...
genome assemblies. By circumventing the problem of haplotype separation through sequencing of fully homozygous hydatidiform mole cell lines5,6, one can achieve highly contiguous assemblies, which, in some instances, traverse centromeric regions7. For diploid samples, haplotype separation has been ...