Increasing evidence suggests that microbial species have a strong within species genetic
heterogeneity. This can be problematic for the analysis of prokaryote genomes, which …

The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in
large-scale microbial analysis. Though mapping approaches can be used to find differences …

Whole‐genome sequencing of prokaryotes is now readily available and affordable on next‐
generation sequencing platforms. However, the process of de novo assembly can be …

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 …

Advances in modern sequencing technologies allow us to generate sufficient data to
analyze hundreds of bacterial genomes from a single machine in a single day. This potential …

Motivation Genome sequencing projects sometimes uncover more organisms than
expected, especially for complex and/or non-model organisms. It is therefore useful to …

Background Bacterial gene loss and acquisition is a well-known phenomenon which
contributes to bacterial adaptation through changes in important phenotypes such as …

BugBuilder is a framework for hands-free assembly and annotation of microbial genomes. It
produces outputs suitable either for database submission or downstream finishing …

Background Inconsistencies are often observed in the genome annotations of bacterial
strains. Moreover, these inconsistencies are often not reflected by sequence discrepancies …

Bacterial genomes are simpler than mammalian ones, and yet assembling the former from
the data currently generated by high-throughput short-read sequencing machines still …