ArticleNature methods2016
Phased diploid genome assembly with single-molecule real-time sequencing.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,095 papers.
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Who cites it
1,095 citing papers in PubMed.
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- Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's disease in Vitis arizonica and its hybrids.G3 (Bethesda, Md.) · 2026Article
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- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- The impact of drought stress on the physiological biochemical indexes and metabolites in Panax notoginseng.Scientific reports · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- Complete genome sequence of the endophyticMicrobiology resource announcements · 2026Article
1,035 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
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.
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