Defense systems

The results of running DefenseFinder v1.3.0 on all Enterobacterales species with >400 samples from release 0.2 plus incremental release 2024-08 are available on OSF in the DefenseFinder component. This includes 27 species and 1,166,956 samples.

Note that this analysis is all with DefenseFinder v1.3.0 using the profiles from defense-finder-models v1.3.0 and CasFinder v3.1.0. This means that defense systems added to DefenseFinder after July 2024 will not be present in the results. the time of writing (February 2026) the latest release of DefenseFinder is v2.0.1

We have shared a single results file which is the concatenated output of the systems.tsv file from all individual DefenseFinder runs. The status file indicates which samples we ran the analysis on with PASS if the run completed successfully. There are n=653 samples where no defense system was detected in the assembly, so these samples are absent from the results file but coded as PASS in the status file.

Important: Note that this analysis is all with DefenseFinder v1.3.0 using the profiles from CasFinder v3.1.0 and defense-finder-models v1.3.0, the latter of which includes 151 defense systems (and 16 anti-defense systems). This means that newer defense systems added to DefenseFinder after July 2024 will not be present in the results. For context, as of February 2026 the latest release of DefenseFinder is v2.0.1 and the latest models version (v2.0.2) contains 262 defense systems.

More details on the analysis are available on the AllTheBacteria github here.