Identification of genetic variations is a central part of population and quantitative genomics
studies based on high-throughput sequencing data. Even though popular variant callers …

Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and
microbial genetics. Its capacity to produce long reads in real time has opened up unique …

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 …

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-
funded international consortia, have become increasingly affordable, thus fitting the budgets …

Transposable elements are ubiquitous mobile DNA sequences generating insertion
polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to …

The quality of genome assemblies has improved rapidly in recent years due to continual
advances in sequencing technology, assembly approaches, and quality control. In the field …

MUM&Co is a single bash script to detect structural variations (SVs) utilizing whole-genome
alignment (WGA). Using MUMmer's nucmer alignment, MUM&Co can detect insertions …

Motivation Nanopore sequencing is one of the leading third-generation sequencing
technologies. A number of computational tools have been developed to facilitate the …

Abstract Summary Bacterial Healthcare-Associated Infections (HAIs) are a major threat
worldwide, which can be counteracted by establishing effective infection control measures …

Whole genome sequencing has revolutionized infectious disease surveillance for tracking
and monitoring the spread and evolution of pathogens. However, using a linear reference …