{
  "default_panel": "202309",
  "panels": {
    "bradley-2015": {
      "description": "AMR panel described in Bradley, P et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat. Commun. 6:10063 doi: 10.1038/ncomms10063 (2015)",
      "kmer": 21,
      "fasta_files": [
        "tb-species-170421.fasta.gz",
        "tb-bradley-probe-set-jan-2019.fasta.gz"
      ],
      "json_files": {
        "amr": "variant_to_resistance_drug.json",
        "lineage": null,
        "hierarchy": "mtbc_hierarchy.json"
      },
      "reference_genome": "NC_000962.3",
      "species_phylo_group": "Mycobacterium_tuberculosis_complex"
    },
    "walker-2015": {
      "description": "AMR panel described in Walker, Timothy M et al. Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study. The Lancet Infectious Diseases , Volume 15 , Issue 10 , 1193 - 1202",
      "kmer": 21,
      "fasta_files": [
        "tb-species-170421.fasta.gz",
        "tb-walker-probe-set-jan-2019.fasta.gz"
      ],
      "json_files": {
        "amr": "variant_to_resistance_drug.json",
        "lineage": null,
        "hierarchy": "mtbc_hierarchy.json"
      },
      "reference_genome": "NC_000962.3",
      "species_phylo_group": "Mycobacterium_tuberculosis_complex"
    },
    "201901": {
      "description": "AMR panel based on first line drugs from NEJM-2018 variants (DOI 10.1056/NEJMoa1800474), and second line drugs from Walker 2015 panel",
      "kmer": 21,
      "fasta_files": [
        "tb-species-170421.fasta.gz",
        "tb-hunt-probe-set-jan-03-2019.fasta.gz"
      ],
      "json_files": {
        "amr": "variant_to_resistance_drug-jan-03-2019.json.gz",
        "hierarchy": "mtbc_hierarchy.json"
      },
      "reference_genome": "NC_000962.3",
      "species_phylo_group": "Mycobacterium_tuberculosis_complex"
    },
    "202010": {
      "description": "AMR panel based on first line drugs from NEJM-2018 variants (DOI 10.1056/NEJMoa1800474), second line drugs from Walker 2015 panel, and lineage scheme from Chiner-Oms 2020",
      "kmer": 21,
      "fasta_files": [
        "tb-species-170421.fasta.gz",
        "tb-hunt-probe-set-jan-03-2019.fasta.gz",
        "tb.lineage.20200930.probes.fa.gz"
      ],
      "json_files": {
        "amr": "variant_to_resistance_drug-jan-03-2019.json.gz",
        "lineage": "tb.lineage.20200930.json",
        "hierarchy": "mtbc_hierarchy.json"
      },
      "reference_genome": "NC_000962.3",
      "species_phylo_group": "Mycobacterium_tuberculosis_complex"
    },
    "202206": {
      "description": "AMR panel '202010' combined with the WHO 2021 catalogue (doi:10/h298 and doi:10/h299), and lineage scheme from Chiner-Oms 2020",
      "kmer": 21,
      "fasta_files": [
        "tb-species-170421.fasta.gz",
        "tb-probe-set-202206.fasta.gz",
        "tb.lineage.20200930.probes.fa.gz",
        "tb-lineage-bcg-rd1.fasta.gz"
      ],
      "json_files": {
        "amr": "variant_to_resistance_drug-202206.json.gz",
        "lineage": "tb.lineage.202206.json",
        "hierarchy": "mtbc_hierarchy.json"
      },
      "reference_genome": "NC_000962.3",
      "species_phylo_group": "Mycobacterium_tuberculosis_complex"
    },
    "202309": {
      "description": "AMR panel '202010' combined with the WHO 2021 catalogue (doi:10/h298 and doi:10/h299), lineage scheme from Chiner-Oms 2020, and updated species based on GTDB r214 (doi:10.1093/nar/gkab776)",
      "kmer": 21,
      "fasta_files": [
        "tb-species-202309.fasta.gz",
        "tb-probe-set-202206.fasta.gz",
        "tb.lineage.20200930.probes.fa.gz",
        "tb-lineage-bcg-rd1.fasta.gz"
      ],
      "json_files": {
        "amr": "variant_to_resistance_drug-202206.json.gz",
        "lineage": "tb.lineage.202206.json",
        "ncbi_names": "ncbi_names.202309.json",
        "hierarchy": "mtbc_hierarchy.202309.json"
      },
      "reference_genome": "NC_000962.3",
      "species_phylo_group": "Mycobacterium_tuberculosis_complex"
    }
  },
  "species_name": "tb",
  "version": "20230928"
}
