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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
TLDR
The development of an algorithm for genome assembly, ALLPATHS-LG, and its application to massively parallel DNA sequence data from the human and mouse genomes, generated on the Illumina platform, have good accuracy, short-range contiguity, long-range connectivity, and coverage of the genome.
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Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
TLDR
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, so genome-wide chromatin interaction data sets, such as those generated by Hi-C, are a rich source of long-range information for assigning, ordering and orienting genomic sequences to chromosomes, including across centromeres.
View on Nature
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
TLDR
This assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.
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The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
TLDR
Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis.
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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
TLDR
This study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care.
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ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
TLDR
Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds.
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Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps
TLDR
It is shown that the Hi-C signal can be used to create scaffolded genome assemblies of individual eukaryotic species present within the microbial community, with higher levels of contiguity than some of the species’ published reference genomes.
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In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.
TLDR
It is demonstrated that fragScaff is complementary to Hi-C-based contact probability maps, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.
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Accurate identification of centromere locations in yeast genomes using Hi-C
TLDR
A method is described, Centurion, that jointly infers the locations of all centromeres in a single genome from Hi-C data by exploiting the centromres’ tendency to cluster in three-dimensional space and is shown to be robust in datasets with low sequencing depth.
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Targeted enrichment and high-resolution digital profiling of mitochondrial DNA deletions in human brain
TLDR
It is demonstrated that the total deletion load increases with age, while the total number and diversity of unique deletions remain constant, providing support for the hypothesis that expansion of pre‐existing mutations is the primary factor contributing to age‐related accumulation of mtDNA deletions.
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