Species specific typing

Summary

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

For standard MLST queries across the aggregated ATB metadata up to and including 2025-05, use atb mlst:

atb fetch

# Get MLST calls for high-quality E. coli genomes
atb mlst --species "Escherichia coli" --hq-only --limit 20

# Find a sequence type
atb mlst --species "Escherichia coli" --st 131 --hq-only

# Query by scheme
atb mlst --scheme salmonella --limit 50

# Download matching assemblies
atb mlst --species "Escherichia coli" --st 131 --download -d ./st131

The sections below describe species-specific typing analyses that go beyond the standard MLST table, such as capsule, toxin, serotype, and lineage 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