AllTheBacteria - all bacterial genomes assembled, available and searchable

The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassembled or inconsistently assembled and QC-ed. This makes it unsuitable for large-scale analyses, and inaccessible for most researchers to use. In 2021 Blackwell et al therefore released a uniformly assembled set of 661,405 genomes, consisting of all publicly available whole genome sequenced bacterial isolate data as of November 2018, along with various search indexes. In this study we extend that dataset by 4.5 years (up to May 2023), tripling the number of genomes. We also expand the scope, as we begin a global collaborative project to generate annotations for different species as desired by different research communities.

In this study we describe the initial v0.1 data release of 1,932,812 assemblies (combining 1,271,428 new assemblies with the 661k dataset). All 1.9 million have been uniformly re-processed for quality criteria and to give taxonomic abundance estimates with respect to the GTDB phylogeny. Using an evolution-informed compression approach, the full set of genomes is just 102Gb in batched xz archives. We also provide multiple search indexes. Finally, we outline plans for future annotations to be provided in further releases.