ArticleGenome research2017
Direct determination of diploid genome sequences.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 471 papers.
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Who cites it
471 citing papers in PubMed.
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- A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape.Innovation (Cambridge (Mass.)) · 2026Article
- Draft assemblies for 177 bird species enhance genus-level coverage.GigaScience · 2026Article
- A comprehensive reference genome assembly dataset of birds inhabiting Denmark, Greenland, and the Faroe Islands.GigaScience · 2026Article
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- Draft genome of the Crimson rosella (Platycercus elegans elegans), an Australian parrot and key resource for the study of host-pathogen interaction in Psittaciformes.BMC genomic data · 2025Article
- Population Genomics Reveals Local Adaptation Related to Temperature Variation in Two Stream Frog Species: Implications for Vulnerability to Climate Warming.Molecular ecology · 2025Article
- Life inside a bag: multiomics insights into the bagworm species Eumeta crameri.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Genome assemblies of IndianNAR genomics and bioinformatics · 2025Article
411 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses, and in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed free of reference bias, but nearly all were constructed by merging homologous loci into single "consensus" sequences, generally absent from nature. These assemblies do not correctly represent the diploid biology of an individual. In exactly two cases, true diploid de novo assemblies have been made, at great expense. One was generated using Sanger sequencing, and one using thousands of clone pools. Here, we demonstrate a straightforward and low-cost method for creating true diploid de novo assemblies. We make a single library from ∼1 ng of high molecular weight DNA, using the 10x Genomics microfluidic platform to partition the genome. We applied this technique to seven human samples, generating low-cost HiSeq X data, then assembled these using a new "pushbutton" algorithm, Supernova. Each computation took 2 d on a single server. Each yielded contigs longer than 100 kb, phase blocks longer than 2.5 Mb, and scaffolds longer than 15 Mb. Our method provides a scalable capability for determining the actual diploid genome sequence in a sample, opening the door to new approaches in genomic biology and medicine.
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