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Commit History
5 days ago
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taxonova 26.11.3: short reads (80 to 119 valid bases) are classified, with a note in the results and a hint before the run; pin 26.11.3 Running
MeluXina user4ffc1bd
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 -
Confidence caption: reasons worded as phrases; no 'the others none' when every sequence has a label
43025f9 -
Withheld species calls: count those lost to a higher rank, to rounding or to another rule apart from the gate and the group rule; confidence caption gives the counted reasons per rank
abd0a69 -
Page: file pickers reachable by keyboard, region hint wording, stats in one row, rank labels left-aligned
7dfc239 -
Pin taxonova 26.11.0; Dockerfile asserts the requirements pin and runs parity for every model; README for 26.11
12a6b26 -
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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Region names without repetition
Verified signature69b285b -
Full names always: exact labels, no names switch
Verified signaturef1da1dc -
Reference database selector and per-reference name display
Verified signaturea69199c -
Footer: drop the model line
Verified signaturef66afc2 -
Species-first example data; content-hash cache busting for static files
Verified signature8e7087a -
Composition view opens at species rank
Verified signaturee8bbde8 -
Shorter Greengenes2 names for display, with a switch for full names
Verified signature2ac3ae7 -
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