Background Third-generation single molecule sequencing technologies can sequence long
reads, which is advancing the frontiers of genomics research. However, their high error rates …

Motivation Structural variants are defined as genomic variants larger than 50 bp. They have
been shown to affect more bases in any given genome than single-nucleotide …

Motivation Recent advances in high-throughput long-read sequencers, such as PacBio and
Oxford Nanopore sequencers, produce longer reads with more errors than short-read …

Whole-genome sequencing using sequencing technologies such as Illumina enables the
accurate detection of small-scale variants but provides limited information about haplotypes …

Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing
transcriptome analysis through its capacity to sequence the majority of transcripts from end …

Long-read sequencers, such as Pacific Biosciences (PacBio) and Oxford Nanopore
Technologies (ONT) sequencers, have improved their read length and accuracy, thereby …

In silico approaches for next-generation sequencing (NGS) data modeling have utility in the
clinical laboratory as a tool for clinical assay validation. In silico NGS data can take a variety …

Background Advancements in metagenomics sequencing allow the study of microbial
communities directly from their environments. Metagenomics binning is a key step in the …

Whole-genome sequencing is increasingly used to identify Mendelian variants in clinical
pipelines. These pipelines focus on single-nucleotide variants (SNVs) and also structural …

Accurate simulations of structural variation distributions and sequencing data are crucial for
the development and benchmarking of new tools. We develop Sim-it, a straightforward tool …