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  1. KmerAperture KmerAperture Public

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

    Python 6

  2. BactCore BactCore Public

    Rapidly extract a flexible bacterial core genome alignment

    C++ 2

  3. BactVar BactVar Public

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

    Python