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brucetyper

In silico Bruce-ladder, Suis-ladder, AMOS PCR and an RB51 junction PCR for Brucella, run end to end from assembled genomes.

For every FASTA file the primer pairs of each requested assay are located directly in the nucleotide sequence, the resulting amplicon sizes are read the way a gel would be read, and a genotype is called. No external PCR tool, no alignment step, no database.

Pages

• Installation — pip, pipx, from a clone, and what gets installed
• Usage — inputs, every command line option, and the three reports that come out
• Methods — how observed sizes become canonical bands, how a profile is matched, and how the rough flag is read
• The assays — what each assay resolves, what it cannot, the RB51 junction assay in detail, and the publications
• Validation — every primer checked against its publication and every band size against 87 real genomes, including the primer sets that were checked and rejected
• Large scale validation — all 2051 GenBank assemblies under taxid 234 through all four assays: concordance with the submitted labels, what the disagreements actually are, and zero calls on the 333 Ochrobactrum-derived genomes
• Development — the test suite and the legacy 2023 scripts

At a glance

Assay	Flag	Separates
Bruce-ladder	--bruce	All Brucella species, plus the S19 and RB51 vaccine strains
Suis-ladder	--suis	B. suis biovars 1 to 5, and suis from canis
AMOS PCR	--amos	abortus bv 1/2/4, melitensis, ovis, suis bv 1, S19
RB51 junction	--rb51	RB51 from its parent 2308, which no other assay here does

These pages are generated from docs/wiki in the repository. Edit them there, not in the wiki, or the next sync will overwrite your changes.