snippy 4.6.0+dfsg-2 (amd64 binary) in ubuntu lunar

 Snippy finds SNPs between a haploid reference genome and your NGS
 sequence reads. It will find both substitutions (snps) and
 insertions/deletions (indels). It will use as many CPUs as you can give
 it on a single computer (tested to 64 cores). It is designed with speed
 in mind, and produces a consistent set of output files in a single
 folder. It can then take a set of Snippy results using the same
 reference and generate a core SNP alignment (and ultimately a
 phylogenomic tree).