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

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

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 Microbial genomes are largely comprised of protein coding sequences, yet
some genomes contain many pseudogenes caused by frameshifts or internal stop codons …

Few discoveries have been more transformative to the biological sciences than the
development of DNA sequencing technologies. The rapid advancement of sequencing and …

Background Parameters adversely affecting the contiguity and accuracy of the assemblies
from Illumina next-generation sequencing (NGS) are well described. However, past studies …

Background Across the fully sequenced microbial genomes there are thousands of
examples of overlapping genes. Many of these are only a few nucleotides long and are …

Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may
occur as a result of shifts in environment leading to changes in the intensity and/or …

We tested the capabilities of four different software tools to detect insertions and deletions
(indels) in a bacterial genome on the basis of short sequencing reads. We included tools …

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 …