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Benchmarking datasets for assembly-based variant calling using high-fidelity long reads
BackgroundRecent advances in long-read sequencing technologies have enabled accurate identification of all genetic variants in individuals or cells;...
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Uncovering the photosystem I assembly pathway in land plants
Photosystem I (PSI) is one of two large pigment–protein complexes responsible for converting solar energy into chemical energy in all oxygenic...
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Visualizing chaperone-mediated multistep assembly of the human 20S proteasome
Dedicated assembly factors orchestrate the stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP)...
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Local eukaryotic and bacterial stream community assembly is shaped by regional land use effects
With anticipated expansion of agricultural areas for food production and increasing intensity of pressures stemming from land-use, it is critical to...
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High-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an...
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Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
Potato is one of the world’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a...
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Haplotype-resolved assembly of a pig genome using single-sperm sequencing
Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed...
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Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly
Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers...
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Mabs, a suite of tools for gene-informed genome assembly
BackgroundDespite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds...
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NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads
Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we...
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Higher-order protein assembly controls kinetochore formation
To faithfully segregate chromosomes during vertebrate mitosis, kinetochore–microtubule interactions must be restricted to a single site on each...
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Sequencing and Assembly of Polyploid Genomes
Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations...
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Biotemplated precise assembly approach toward ultra-scaled high-performance electronics
Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and...
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Landscape matrix and substrate jointly shape the trait composition of true bug (Heteroptera) communities in drainage ditches
Drainage ditches play a key role in the conservation of fragmented landscapes by providing refuge sites and secondary habitats for many terrestrial...
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Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease
Isolated complex I (CI) deficiencies are a major cause of primary mitochondrial disease. A substantial proportion of CI deficiencies are believed to...
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Soil nitrogen deficiency drives compensatory assembly of nitrogen-cycling functions in the rhizosphere microbiome
Backgrounds and aimsPlant rhizosphere microbiome play crucial roles in plant growth. However, the mechanisms governing the rhizosphere microbiome...
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Forest gaps increase true bug diversity by recruiting open land species
Forests canopy gaps play an important role in forest ecology by driving the forest mosaic cycle and creating conditions for rapid plant reproduction...
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Genome sequence assembly algorithms and misassembly identification methods
The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. Assembly...
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Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly
BackgroundDiverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production...
