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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
Massively parallel DNA sequencing technologies are revolutionizing genomics by making it possible to generate billions of relatively short (~100-base) sequence reads at very low cost. Whereas suchExpand
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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
Genomes assembled de novo from short reads are highly fragmented relative to the finished chromosomes of Homo sapiens and key model organisms generated by the Human Genome Project. To address thisExpand
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Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However,Expand
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The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro. TheExpand
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A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota
Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here,Expand
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Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
Microbial communities consist of mixed populations of organisms, including unknown species in unknown abundances. These communities are often studied through metagenomic shotgun sequencing, butExpand
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In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.
We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means ofExpand
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Accurate identification of centromere locations in yeast genomes using Hi-C
Centromeres are essential for proper chromosome segregation. Despite extensive research, centromere locations in yeast genomes remain difficult to infer, and in most species they are still unknown.Expand
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Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain
Due largely to the inability to accurately quantify and characterize de novo deletion events, the mechanisms underpinning the pathogenic expansion of mtDNA deletions in aging and neuromuscularExpand
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Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi‐C
Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbialExpand
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