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Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nanopore sequencing and assembly of a human genome with ultra-long reads. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Phased diploid genome assembly with single-molecule real-time sequencing. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology (Cambridge Univ. Recurrent inversion with concomitant deletion and insertion events in the coagulation factor VIII gene suggests a new mechanism for X-chromosomal rearrangements causing hemophilia A. Mechanisms underlying structural variant formation in genomic disorders. Pelizaeus-Merzbacher disease caused by a duplication-inverted triplication-duplication in chromosomal segments including the PLP1 region. Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Resolving the complexity of the human genome using single-molecule sequencing.
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Minimap2: fast pairwise alignment for long nucleotide sequences. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. Adaptive seeds tame genomic sequence comparison. Coming of age: ten years of next-generation sequencing technologies. On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Detection of genomic structural variants from next-generation sequencing data. Mapping copy number variation by population-scale genome sequencing. PBHoney: identifying genomic variants via long-read discordance and interrupted mapping. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. DELLY: structural variant discovery by integrated paired-end and split-read analysis. LUMPY: a probabilistic framework for structural variant discovery. Genome structural variation discovery and genotyping. Exome sequence read depth methods for identifying copy number changes. Large-scale copy number polymorphism in the human genome. Genomic rearrangements in Arabidopsis considered as quantitative traits. Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. An integrated map of structural variation in 2,504 human genomes. APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy.
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Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci. Sequencing structural variants in cancer for precision therapeutics. Structural variation mutagenesis of the human genome: impact on disease and evolution. Phenotypic impact of genomic structural variation: insights from and for human disease. Weischenfeldt, J., Symmons, O., Spitz, F. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches.
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Addressing this need, we introduce open-source methods for long-read alignment (NGMLR ) and structural variant identification (Sniffles ) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations.