Generating complete, high-quality genome assemblies is key for any downstream analysis,
such as comparative genomics. For bacterial genome assembly, various algorithms and fully …

Background De novo genome assembly can be challenging due to inherent properties of
the reads, even when using current state-of-the-art assembly tools based on de Bruijn …

Next-generation sequencing methods provide comprehensive data for the analysis of
structural and functional analysis of the genome. The draft genomes with low contig number …

Background Accurate bacteria genome de novo assembly is fundamental to understand the
evolution and pathogenesis of new bacteria species. The advent and popularity of Third …

Motivation: A crucial problem in genome assembly is the discovery and correction of
misassembly errors in draft genomes. We develop a method called misSEQuel that …

The uncurated genome assembly data often contains DNA contaminations, originated from
exotic organisms, introduced during DNA extraction or sequencing. It happens sometimes …

High-throughput comparative genomics has changed our view of bacterial evolution and
relatedness. Many genomic comparisons, especially those regarding the accessory genome …

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

Motivation Long-read genome assembly tools are expected to reconstruct bacterial
genomes nearly perfectly; however, they still produce fragmented assemblies in some …

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses,
but short reads (< 300 bp) do not usually enable complete genome assembly. Long-read …