BrucellaID 2.2.0

The extended reference set changes, so some samples change their call. It is now 429 genomes instead of 432, and sixteen of them carry a different label. Distances do not change: a sample's distance to a reference does not depend on what else the sketch holds, and the 429 remaining genomes are in the rebuilt sketch with exactly the hashes they had.

A sample can now be reported under a species name that does not begin with Brucella. Ochrobactrum teleogrylli and O. chromiisoli were described after Ochrobactrum was moved into Brucella, nobody has published a Brucella combination for either, and NCBI files both outside the genus. Four genomes of the set are theirs, at 98.1–99.2% ANI to the type strains, and are labelled with the names the species have. Anything that parses the Species column on the assumption that it starts with "Brucella" should be checked.

Eleven unnamed genomes take the name of the Brucella species they belong to. They were Brucella sp. and are 96.2–99.3% ANI from a type strain, measured in both directions: one B. tritici, three B. anthropi, two B. intermedia, one B. haematophila and four B. pseudogrignonensis. A sample matching one was reported as Brucella sp. and is now reported under its species.

GCA_900095155.1 is now Brucella sp., not B. inopinata. It is 97.87% ANI from the B. inopinata type strain BO1, further than three references the set already called Brucella sp.

Three partial genomes are removed: GCA_040391195.1, GCA_032085995.1 and GCA_032104425.1, each 2.1 to 3.7 Mb of a species of about 5 Mb that the set holds complete genomes of. None was the best match of any identified run among 4,024 public read sets. A custom --references table written against the 432 will name three genomes the sketch no longer holds, which BrucellaID reports at start-up.

What it changes in practice

Population	Calls that change
The 4,024 usable public Brucella read sets in ENA	four: SRR12605656, SRR25828924 and SRR25828932 go from Brucella sp. to O. teleogrylli, and SRR12224742 from B. inopinata to Brucella sp.
1,543 held-out simulated samples of a named species	none

The 16-genome vSNP set (--reference-set vsnp) is untouched.

Arbitration also reaches fewer references. Genome against genome, a second species falls inside the close-match margin of 33 of the 429 references across 10 species pairs, where it was 38 across 14: four of those pairs were a named species against one of its own unnamed genomes.

The evidence for every relabel and removal is in curation/unnamed_lineages.md, and each decision is a row of scripts/extended_references_curation.tsv.

Also in this release

• The at-scale validation is re-measured under the shipped k-mer copy threshold. All 4,024 public read sets were swept again against both reference sets. The headline figures are unchanged: the extended set matches the submitter on 98.7% and the vSNP set on 96.2%.
• --loose-distance 0.001 is confirmed on all 4,001 identified runs, where the 95th percentile of agreeing calls is 0.00068.
• One claim is withdrawn. Agreement with the submitter is not flat in distance: it falls from 99.5% on close calls to 81.2% between 0.005 and 0.02.
• A warning for ENA's three-file runs. find_samples() now warns when a _3 fastq sits beside a pair it has formed: in that layout _1 holds the unpaired reads and _2/_3 are the mates.
• A stale sentence on the validation page is corrected: of the 95 unnamed simulated samples, 37 are reported as Brucella sp. and 56 under a name.

The full entry is in the changelog.