Bacterial genome sequencing is the determination of the sequence of nucleic acids in genomic DNA of bacteria using DNA sequencing techniques. The first bacterial genomes to have complete sequences were Haemophilis influenze and Mycoplasm genitalium, published in 1995. By 2017 about 12,300 bacterial genomes had been sequenced. Bacterial genome sequences are publicly available at the NCBI Microbial Genomes page, the Genomes OnLine Database (GOLD) and Sequence Read Archive (SRA).
Bacterial genomes were mostly sequenced by the Sanger method prior to 2005 using whole genome shotgun libraries and capillary electrophoresis. This required assembly of sequences into a draft genome that was then finished. The cost of a finished bacterial genome was about $50,000. Next-Generation Sequencing (NGS), also known as second generation sequencing, allowed low-cost, high-throughput sequencing to be available to commercial vendors. In 2015 it was estimated that the cost of generating a draft bacterial genome can be less than $1. NGS technology such as Illumina produced shorter reads than Sanger sequencing which meant that the cost of the finishing steps, after the draft is complete, could be 95% of the total. Due to the cost of finishing, many genomes are published in draft status, in multiple contigs and varying quality.
