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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule,
Phased diploid genome assembly with single-molecule real-time sequencing
TLDR
The open-source FALCON and FALcon-Unzip algorithms are introduced to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes.
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
TLDR
The MinHash Alignment Process (MHAP) is introduced for overlapping noisy, long reads using probabilistic, locality-sensitive hashing and can produce de novo near-complete eukaryotic assemblies that are 99.99% accurate when compared with available reference genomes.
Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
TLDR
The findings suggest that horizontal genetic exchange allowed for the emergence of the highly virulent Shiga-toxin-producing enteroaggregative E. coli O104:H4 strain that caused the German outbreak, and highlight the way in which the plasticity of bacterial genomes facilitates the emerged of new pathogens.
Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia
TLDR
It is demonstrated that FLT3-ITD can represent a driver lesion and valid therapeutic target in human AML and AC220-resistant FLT 3 kinase domain mutants represent high-value targets for futureFLT3 inhibitor development efforts.
Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
TLDR
The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches, and enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.
The origin of the Haitian cholera outbreak strain.
TLDR
The Haitian epidemic is probably the result of the introduction, through human activity, of a V. cholerae strain from a distant geographic source, and analysis of genomic variation of the Haitian isolates reveals a more distant relationship with circulating South American isolates.
Improved maize reference genome with single-molecule technologies
TLDR
The assembly and annotation of a reference genome of maize is reported, using single-molecule real-time sequencing and high-resolution optical mapping to identify transposable element lineage expansions that are unique to maize.
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
TLDR
It is asserted that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote the understanding of human biology and advance the efforts to improve health.
Assembly and diploid architecture of an individual human genome via single-molecule technologies
TLDR
This work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.
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