Species specific typing

Summary

All sylph-identified genomes from AllTheBacteria 0.2 and incremental release 2024-08 were typed using various tools

Bacillus cereus group spp.

• BTyper3 v3.4.0 (Standardized taxonomic classification and sequence typing, detection of virulence and Bt toxin-encoding genes)
• Result files are available on OSF in the Bacillus_cereus_group component.

Bordetella pertussis

• mlst schema 2024-06-10
• BPagST schema downloaded 2024-06-10

Corynebacterium diphtherieae

• mlst schema 2024-06-10
• Toxin

Haemophilus spp.

• mlst schema 2024-06-10
• hicap v1.0.4 (capsule)

Klebsiella spp.

• Kleborate v2.3.2 (MLST, virulence, capsule, antimicrobial resistance)

Legionella pneumophila

• legsta v0.5.1 (SBT)

Mycobacterium tuberculosis

• TBProfiler v6.2.1 (spoligotyping, lineage, antimicrobial resistance)

Neisseria gonorrhoeae

• pyngoST v1.1.2 (MLST, NG-MAST, NG-STAR, penA)

Neisseria meingitidis

• meningotype v0.8.5 (MLST, serotype, Finetype, Bexsero antigen typing, MenDeVAR Index)

Streptococcus agalactiae (GBS)

• mlst schema 2024-06-10
• GBS-SBG (git commit 9e53847) (capsule)

Streptococcus pneumoniae

• mlst schema 2024-06-10
• PneumoKITy v1.0 (capsule)

Streptococcus pyogenes (GAS)

• mlst schema 2024-06-10
• emm-typer v0.2.0
• assembly_typer v0.1.0 (M1UK, M1DK)