![]() Genome sequences are typically determined by a shotgun approach where sequence reads are generated from random places in the genome using one out of a limited number of available sequencing technologies ( Heather and Chain, 2016). Thus, the focus of this mini review is to use the representation in the genome databases to give an overview of sequencing technologies and assembly methods that are or have been in active use specifically for bacterial WGS. A historical perspective is also given by comparing different time segments of the databases. ![]() It summarizes and briefly describes methods which are frequently reported as being used in the RefSeq and surveillance sections of the GenBank bacterial genome database. This mini review focuses on two important aspects (i) sequencing technology usage and (ii) genome assembly software usage. Setting up a capacity to perform bacterial whole genome sequencing (WGS) requires many technical considerations. In all, this mini review provides an overview of the currently most common workflows for producing bacterial whole genome sequence assemblies. 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. Information associated with over 400,000 publically available genomes dated April 2020 and prior were used. The data is presented both in total and broken up on a per year basis. 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. To accomplish this, a number of different sequencing technologies and assembly methods are available. Many whole genome analysis workflows begins with the production of a genome assembly. Whole genome sequencing is not only used in research projects, but also in surveillance projects and outbreak investigations. Especially bacterial genomes are sequenced in high numbers. Whole genome sequencing has become a powerful tool in modern microbiology. 2Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.1Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden.
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