The Most Frequently Used Sequencing Technologies and Assembly Methods in Different Time Segments of the Bacterial Surveillance and RefSeq Genome Databases

Whole genome sequencing has become a powerful tool in modern microbiology. Especially bacterial genomes are sequenced in high numbers. Whole genome sequencing is not only used in research projects, but also in surveillance projects and outbreak investigations. Many whole genome analysis workflows begins with the production of a genome assembly. To accomplish this, a number of different sequencing technologies and assembly methods are available. Here, a summarization is provided over the most frequently used sequence technology and genome assembly approaches reported for the bacterial RefSeq genomes and for the bacterial genomes submitted as belonging to a surveillance project. The data is presented both in total and broken up on a per year basis. Information associated with over 400,000 publically available genomes dated April 2020 and prior were used. The information summarized include (i) the most frequently used sequencing technologies, (ii) the most common combinations of sequencing technologies, (iii) the most reported sequencing depth, and (iv) the most frequently used assembly software solutions. In all, this mini review provides an overview of the currently most common workflows for producing bacterial whole genome sequence assemblies.