mykrobe

Mykrobe

Mykrobe and Dr. PRG are run on Mycobacterium. Mykrobe has more extensive analyses available for non-TB Mycobacterium (NTM).

About: |

Antibiotic resistance prediction in minutes.

Documentation : https://github.com/Mykrobe-tools/mykrobe/wiki

Citation : https://doi.org/10.12688/wellcomeopenres.15603.1

Directory tree:

mykrobe/
├── sample.csv
├── sample.json
└── mykrobe_summary.csv

Example file for an individual sample (sample.csv) - there is also a sample.json file

"sample","drug","susceptibility","variants (dna_variant-AA_variant:ref_kmer_count:alt_kmer_count:conf) [use --format json for more info]","genes (prot_mut-ref_mut:percent_covg:depth) [use --format json for more info]","mykrobe_version","files","probe_sets","genotype_model","kmer_size","phylo_group","species","lineage","phylo_group_per_covg","species_per_covg","lineage_per_covg","phylo_group_depth","species_depth","lineage_depth"
"myco_GCF_000195955.2","NA","N","","","v0.13.0","myco_GCF_000195955.2.fasta","/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb-species-202309.fasta.gz;/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb-probe-set-202206.fasta.gz;/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb.lineage.20200930.probes.fa.gz;/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb-lineage-bcg-rd1.fasta.gz","kmer_count","21","Mycobacterium_tuberculosis_complex","Mycobacterium_tuberculosis","lineage4.10","100.0","100.0","NA","1.0","1","NA"

Example file for a run (mykrobe_summary.csv)

"sample","drug","susceptibility","variants (dna_variant-AA_variant:ref_kmer_count:alt_kmer_count:conf) [use --format json for more info]","genes (prot_mut-ref_mut:percent_covg:depth) [use --format json for more info]","mykrobe_version","files","probe_sets","genotype_model","kmer_size","phylo_group","species","lineage","phylo_group_per_covg","species_per_covg","lineage_per_covg","phylo_group_depth","species_depth","lineage_depth"
"myco_GCF_000195955.2","NA","N","","","v0.13.0","myco_GCF_000195955.2.fasta","/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb-species-202309.fasta.gz;/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb-probe-set-202206.fasta.gz;/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb.lineage.20200930.probes.fa.gz;/opt/conda/envs/mykrobe/lib/python3.10/site-packages/mykrobe/data/tb/tb-lineage-bcg-rd1.fasta.gz","kmer_count","21","Mycobacterium_tuberculosis_complex","Mycobacterium_tuberculosis","lineage4.10","100.0","100.0","NA","1.0","1","NA"