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Commit History
9 days ago
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Greengenes2 only: one Region list with the reference named under it; SILVA and RDP removed from README, comments, tests and the V4-V5 parity fixture
Taxonova 26.11.1 offers Greengenes2 2024.09 (V4, V4-V5, V3-V4, V5-V7, whole 16S) and the GROND operon model. The reference selector is replaced by one Region list; the line under it names the reference of the chosen model. The V4-V5 parity fixture keeps its 66 Greengenes2 reads and their 3 mutated copies. A test checks that the 26.11.0 SILVA and RDP ids and file names are unknown to the web app. The Dockerfile asserts that the models directory holds exactly the files the registry lists.2a0d367
10 days ago
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Unknown at a rank counts as no name in the reference: apart from the named taxa and from Unclassified in the summary, the confidence caption and the charts (dark grey); downloads unchanged
135bd2c -
Page: file pickers reachable by keyboard, region hint wording, stats in one row, rank labels left-aligned
7dfc239 -
Page: model's own thresholds by default, custom confidence opt-in; region hint lists regions it cannot separate
- threshold panel shows the selected model's operating point, species gate and species-group rule; a species confidence is sent only when chosen - results state the thresholds used and their source, and count species calls withheld by the gate - confidence chart colours sequences by whether they have a label at the rank, not by the threshold alone - region hint: primer, then measured length windows; V4 and V4-V5 (shared primer) and V4-V5 and V5-V7 (same length) are listed together when the reads do not separate them - command-line snippet pins the installed taxonova versionaa59ee1
15 days ago
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Reference database selector and per-reference name display
Verified signaturea69199c -
New web app: composition plots, count tables, downloads; taxonova 26.10.1
Verified signatureRedesigned interface with an example dataset, composition, hierarchy and confidence plots, optional ASV count table for per-sample composition, and TSV, QIIME 2 and phyloseq downloads. Installs taxonova==26.10.1 and uses the short model ids.b018397