Main tool: sistr
Code repository: https://github.com/phac-nml/sistr_cmd
Additional tools:
- blast : 2.9.0
- mafft : v7.453
- mash : 2.2.2
- pandas : 1.0.5
- numpy : 1.23.4
Basic information on how to use this tool:
- executable: sistr
- help: -h, --help
- version: -V, --version
- description: (Salmonella In Silico Typing Resource) Command-line Tool
Full documentation: https://github.com/phac-nml/sistr_cmd
sistr --qc -vv --alleles-output allele-results.json --novel-alleles novel-alleles.fasta --cgmlst-profiles cgmlst-profiles.csv -f tab -o sistr-output.tab genome.fasta