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

{"references": ["http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101"]}