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Whole genome sequencing of simmental cattle for SNP and CNV discovery
BackgroudThe single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in...
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Comparison of structural variant callers for massive whole-genome sequence data
BackgroundDetecting structural variations (SVs) at the population level using next-generation sequencing (NGS) requires substantial computational...
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Targeted next-generation sequencing and long-read HiFi sequencing provide novel insights into clinically significant KLF1 variants
BackgroundKrüppel-like factor 1 (KLF1), a crucial erythroid transcription factor, plays a significant role in various erythroid changes and...
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Long-read PacBio genome sequencing of four environmental saprophytic Sporothrix species spanning the pathogenic clade
BackgroundThe genus Sporothrix belongs to the order Ophiostomatales and contains mainly saprobic soil and plant fungi, although pathogenic species...
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Mutation Mapping and Identification by Whole-Genome Sequencing
Geneticists approach biology with a simple question: which genes are required for the pathway or process of interest? Classical genetic screens (aka...
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Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding
Wheat is a crucial crop globally, with widespread cultivation and significant economic importance. To ensure food security amidst the increasing...
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Recovery and Analysis of Long-Read Metagenome-Assembled Genomes
The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly...
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Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds
Several indigenous cattle breeds in Sweden are endangered. Conservation of their genetic diversity and genomic characterization is a priority.
Whole-ge...
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Structural Variant Detection from Long-Read Sequencing Data with cuteSV
Structural Variation (SV) represents genomic rearrangements and is strongly associated with human health and disease. Recently, long-read sequencing...
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JAFFAL: detecting fusion genes with long-read transcriptome sequencing
In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with...
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Whole genome sequencing analysis of Komagataeibacter nataicola reveals its potential in food waste valorisation for cellulose production
BackgroundKomagataeibacter nataicola ( K. nataicola ) is a gram-negative acetic acid bacterium that produces natural bacterial cellulose (BC) as a...
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The STROMICS genome study: deep whole-genome sequencing and analysis of 10K Chinese patients with ischemic stroke reveal complex genetic and phenotypic interplay
Ischemic stroke is a leading cause of global mortality and long-term disability. However, there is a paucity of whole-genome sequencing studies on...
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A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants
BackgroundPacBio HiFi sequencing provides highly accurate long-read sequencing datasets which are of great advantage for whole genome sequencing...
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Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates
BackgroundOxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However,...
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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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Comprehensive analysis of genomic complexity in the 5’ end coding region of the DMD gene in patients of exons 1–2 duplications based on long-read sequencing
BackgroundDystrophinopathies are the most common X-linked inherited muscle diseases, and the disease-causing gene is DMD . Exonic duplications are a...
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Whole-Genome Sequencing of Plants: Past, Present, and Future
Advances in analytical chemistry, as well as the constant introduction of novel analytical chemistry approaches, are altering genomics at a higher...
