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Full-length isoform concatenation sequencing to resolve cancer transcriptome complexity
BackgroundCancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased...
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Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma
Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome...
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Transcriptome sequencing of seven deep marine invertebrates
We present 4k video and whole transcriptome data for seven deep-sea invertebrate animals collected in the Eastern Pacific Ocean during a research...
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Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms
Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read...
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Next-generation sequencing of newborn screening genes: the accuracy of short-read map**
Newborn screening programs are an integral part of public health systems aiming to save lives and improve the quality of life for infants with...
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A survey of algorithms for the detection of genomic structural variants from long-read sequencing data
As long-read sequencing technologies are becoming increasingly popular, a number of methods have been developed for the discovery and analysis of...
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Using short read sequencing to characterise balanced reciprocal translocations in pigs
BackgroundA balanced constitutional reciprocal translocation (RT) is a mutual exchange of terminal segments of two non-homologous chromosomes without...
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Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients
Inherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified....
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Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing
DNA methylation plays an important role in various biological processes, including cell differentiation, ageing, and cancer development. The most...
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Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and...
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Reconstruction of Archaeal Genomes from Short-Read Metagenomes
As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in...
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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for...
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Computational Pipeline for the Detection of Plant RNA Viruses Using High-Throughput Sequencing
In this chapter, we describe a computational pipeline for the in silico detection of plant viruses by high-throughput sequencing (HTS) from total RNA...
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Beyond assembly: the increasing flexibility of single-molecule sequencing technology
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently,...
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Fast and SNP-aware short read alignment with SALT
BackgroundDNA sequence alignment is a common first step in most applications of high-throughput sequencing technologies. The accuracy of sequence...
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Advances of high-throughput sequencing for unraveling biotechnological potential of microalgal-bacterial communities
Although established biotechnological applications of microalgae e.g., the production of high-value metabolites is based on axenic cultures,...
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Integrative genoty** of cancer and immune phenotypes by long-read sequencing
Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to...
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Detection of four isomers of the human cytomegalovirus genome using nanopore long-read sequencing
Human cytomegalovirus has a linear DNA genome with a total length of approximately 235 kb. This large genome is divided into two domains, "Long" and...
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Benchmarking second and third-generation sequencing platforms for microbial metagenomics
Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities....
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MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
BackgroundWith the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic...
