SPANDx
Comparative analysis of haploid next-generation genome sequence data
...The outputs generated by SPANDx can be imported into PLINK for microbial genome-wide association study (mGWAS) analyses.
SPANDx can utilise PBS, SGE or SLURM for resource management. SPANDx can also run directly on the command line if no resource manager is available.
For the most up-to-date version of SPANDx, check us out on GitHub: https://github.com/dsarov/SPANDx