sistr_cmd v1.0.2 serotyping databases

Salmonella In Silico Typing Resource (SISTR) sistr_cmd version 1.0.2 serotyping databases

File structure tree for sistr_cmd data folder:

.
|-- [4.0K]  antigens
|   |-- [1.0M]  fliC.fasta
|   |-- [210K]  fljB.fasta
|   |-- [126K]  wzx.fasta
|   `-- [ 60K]  wzy.fasta
|-- [4.0K]  cgmlst
|   |-- [7.4M]  cgmlst-centroid.fasta
|   |-- [ 96M]  cgmlst-full.fasta
|   |-- [134M]  cgmlst-profiles.hdf
|   `-- [ 803]  README.md
|-- [1.1M]  genomes-to-serovar.txt
|-- [1.0M]  genomes-to-subspecies.txt
|-- [118K]  Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv
`-- [ 92M]  sistr.msh

2 directories, 12 files

Description of files:

• genomes-to-serovar.txt: Each genome id to serovar designation delimited by tab character for the 52,790 Salmonella genomes.
• genomes-to-subspecies.txt: Each genome id to subspecies designation delimited by tab character for the 52,790 Salmonella genomes.
• Salmonella-serotype_serogroup_antigen_table-WHO_2007.csv: Serovar and antigenic formula information table used by `sistr_cmd` for looking up serovar designations from antigen results
• sistr.msh: Mash sketch file of 11840 Salmonella genomes for Mash-based serotyping
• antigens: for antigen gene search-based serotyping
  • fliC.fasta: fliC gene alleles for H1-antigen typing
  • fljB.fasta: fljB gene alleles for H2-antigen typing
  • wzx.fasta: wzx gene alleles for O-antigen typing
  • wzy.fasta: wzy gene alleles for O-antigen typing
• cgmlst for core-genome multilocus sequence typing (cgMLST) and cgMLST-based serotyping
  • cgmlst-profiles.hdf: HDF5 file with cgMLST allelic profiles of 52,790 Salmonella genomes
    • read in with Pandas, i.e.

      pd.read_hdf(CGMLST_PROFILES_PATH, key='cgmlst')

  • cgmlst-centroid.fasta: "Centroid" or representative alleles of 52,790 Salmonella genomes for rapid NCBI BLAST+ blastn searching. Centroid alleles were defined from the full set of alleles for the 52,790 Salmonella genomes as the alleles for each locus:
    • group alleles by length
    • group length grouped alleles by ends (28bp at allele start and end; 28 is word size of blastn megablast)
    • hierarchical clustering of length+end grouped alleles
    • flat clusters at 2.5% distance
    • within each cluster, pick allele with least distance to others in cluster
• cgmlst-full.fasta: alleles for the 52,790 Salmonella genomes