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BrucellaID

BrucellaID reads a Brucella fastq sample and answers two questions:

• Which species is it? The reads are compared with MASH to 432 curated Brucella genomes covering all 30 named species of the clade, Ochrobactrum included, and the closest one names the species and the reference itself. --reference-set vsnp measures against vSNP's 16 genomes instead, which was the default before 2.0 (How it works).
• Which sequence type is it? The nine alleles of the Whatmore MLST-9 scheme are called from the reads with Seal from BBTools, and looked up in the PubMLST profile table.

Both the reference sketch and the MLST database come with the package: there is nothing to download, index or configure. Where two species are too close for a sketch to choose between them — B. canis and B. suis bv. 4 are 0.00024 apart — the sequence type chooses, and the SpeciesSource column says so.

$ brucellaid -i reads/ -o results/
Sample      Species           SpeciesSource         ClosestReference                           SharedHashes  SequenceType  STSpecies
ERR2136546  Brucella canis    MASH+ST (arbitrated)  GCA_000530495.1_Oliveri_genomic.fna.gz     995/1000      20            Brucella canis
ERR3454415  Brucella abortus  MASH+ST (agree)       GCA_000742195.1_ASM74219v1_genomic.fna.gz  994/1000      1             Brucella abortus

(Two of the four tutorial read sets, against the 432-genome default set. Columns elided to fit; brucellaid.tsv also holds MashDistance, AlleleProfile, Reads and Notes.)

Start here

• Installation — conda, pip, or a clone
• Tutorial — one real sample, start to finish
• Usage — every option
• Output files — what each report holds

Then

• How it works — what the two calls rest on, and where each of them stops
• Validation — 1,543 held-out genomes, 4,024 public read sets, and a 22-sample suite you can re-run, plus the k-mer copy threshold and how it was measured
• Troubleshooting and the FAQ
• Changelog

Citing

Duceppe M-O. BrucellaID: Brucella species identification and MLST from sequencing reads. Zenodo. https://doi.org/10.5281/zenodo.23845956

That DOI resolves to the latest version. Cite it together with the tools and data BrucellaID rests on: MASH, BBTools, the MLST scheme and PubMLST. The full list, ready to paste, is in the README, and GitHub's "Cite this repository" button gives it in APA and BibTeX, from CITATION.cff.