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 …

De novo assembly of bacterial genomes from next-generation sequencing (NGS) data
allows a reference-free discovery of single nucleotide polymorphisms (SNP). However …

We develop a novel mining pipeline, Integrative Next-generation Genome Analysis Pipeline
(inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs) …

A wide variety of genome sequencing platforms have emerged in the recent past. High-
throughput platforms like Illumina and 454 are essentially adaptations of the shotgun …

Motivation The advent of next-generation sequencing has boosted the analysis of bacterial
genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome …

High-throughput sequencing technologies have strongly impacted microbiology, providing a
rapid and cost-effective way of generating draft genomes and exploring microbial diversity …

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 …

The affordability of next generation sequencing (NGS) is transforming the field of mutation
analysis in bacteria. The genetic basis for phenotype alteration can be identified directly by …

Motivation The insertion sequence (IS) elements are the smallest but most abundant
autonomous transposable elements in prokaryotic genomes, which play a key role in …

Background The discovery and mapping of genomic variants is an essential step in most
analysis done using sequencing reads. There are a number of mature software packages …