Background Ongoing technological advances in genome sequencing are allowing bacterial
genomes to be sequenced at ever-lower cost. However, nearly all of these new techniques …

Background The continued democratization of DNA sequencing has sparked a new wave of
development of genome assembly and assembly validation methods. As individual research …

Highlights•We describe three long-read sequencing technologies and their
characteristics.•We describe available algorithms for long-read assembly and their …

Long read sequencing technologies now allow routine highly contiguous assembly of
bacterial genomes. However, because of the lower accuracy of some long read data, it is …

The complexity of genome assembly is due in large part to the presence of repeats. In
particular, large reverse-complemented repeats can lead to incorrect inversions of large …

Gap closure is a challenging phase in microbial random shotgun genome sequencing
projects, particularly since genome assemblies are often complicated by the presence of …

Motivation: Open-source bacterial genome assembly remains inaccessible to many
biologists because of its complexity. Few software solutions exist that are capable of …

The perceived “simplicity” of bacterial genomics (these genomes are small and easy to
assemble) feeds the decentralized state of the field where computational analysis standards …

Background Whole genome sequence construction is becoming increasingly feasible
because of advances in next generation sequencing (NGS), including increasing throughput …

Background De novo genome sequencing of previously uncharacterized microorganisms
has the potential to open up new frontiers in microbial genomics by providing insight into …