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  1. Snitkin-Lab-Umich/ariba_snakemake Snitkin-Lab-Umich/ariba_snakemake Public

    Snakemake pipeline to run ARIBA on genomes using CARD, PlasmidFinder, or MLST database

    Shell 1

  2. Snitkin-Lab-Umich/genome_downloading_snakemake Snitkin-Lab-Umich/genome_downloading_snakemake Public

    Snakemake pipeline to download genomes from NCBI using Biosample Accession Numbers and fasterq-dump

    R 2

  3. Snitkin-Lab-Umich/Snakemake_setup Snitkin-Lab-Umich/Snakemake_setup Public

    Setup information for snakemake pipelines

  4. Snitkin-Lab-Umich/regentrans Snitkin-Lab-Umich/regentrans Public

    regentrans: R package for investigating regional pathogen transmission using genomic data

    R 5 1

  5. ONT_unaligned_meth_calling ONT_unaligned_meth_calling Public

    Chromosome specific methylation calling pipeline

    R