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1. KmerApertureKmerAperturePublic

   Extract SNPs and accessory differences in closely related bacterial genomes from k-mers

   Python 10

2. BactCoreBactCorePublic

   Rapidly extract a flexible bacterial core genome alignment

   C 2

3. BactStreamBactStreamPublic

   Download bacterial genome .fastq files and produce annotated variants one genome at a time

   Python

4. BactVarBactVarPublic

   Map whole bacterial short reads with BWA and call variants with GATK. Outputs SnpEff annotated variants and a whole-genome alignment

   Python