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Use of Whole Genome Sequencing for Mycobacterium tuberculosis Complex Antimicrobial Susceptibility Testing
Whole genome sequencing (WGS) is becoming an important diagnostic tool for antimicrobial susceptibility testing of Mycobacterium tuberculosis complex...
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scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order chromatin structures within individual cells
The high-order three-dimensional (3D) organization of regulatory genomic elements provides a topological basis for gene regulation, but it remains...
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Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over...
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Experimental Approaches to Study Somatic Transposition in Drosophila Using Whole-Genome DNA Sequencing
The extent of transposable element (TE) mobilization in different somatic tissues and throughout diverse species is not well understood. Somatic...
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Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing
BackgroundWhile numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have...
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Whole-Genome Bisulfite Sequencing Protocol for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for...
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Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice
Two decades after the genomics revolution, oncology is rapidly transforming into a genome-driven discipline, yet routine cancer diagnostics is still...
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What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios
When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The...
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How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?
Key messageLong-read sequencing technologies are revolutionizing the sequencing and analysis of plant and pathogen genomes and transcriptomes, as...
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A Simple Cost-Effective Method for Whole-Genome Sequencing, Haplotyping, and Assembly
In this chapter, we describe single-tube long fragment read (stLFR), a simple preparation method for whole-genome sequencing and physical haplotyping...
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Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions
Transposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs...
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Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
BackgroundLong-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher...
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Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
MotivationAlignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained...
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Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution
Copy number variants (CNVs), comprising gene amplifications and deletions, are a pervasive class of heritable variation. CNVs play a key role in...
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Cost-effective library preparation for whole genome sequencing with feather DNA
Samples from avian species of high conservation concern are often low in total genomic DNA (gDNA). Feathers are collected more frequently than blood,...
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Fast and sensitive validation of fusion transcripts in whole-genome sequencing data
BackgroundIn cancer, genomic rearrangements can create fusion genes that either combine protein-coding sequences from two different partner genes or...
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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for...
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A long-read sequencing and SNP haplotype-based novel preimplantation genetic testing method for female ADPKD patient with de novo PKD1 mutation
The autosomal dominant form of polycystic kidney disease (ADPKD) is the most common hereditary disease that causes late-onset renal cyst development...
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Towards reliable whole genome sequencing for outbreak preparedness and response
BackgroundTo understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of...
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Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology
Long-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses,...
