- Dataset card: CC BY-NC 4.0 licence (as the benchmark datasets), layout, file formats, species and sources.
- `reference.gff3.gz` -> `reference_longest_isoform.gff3.gz` (19 folders, server-side copy).
- New `reference_all_isoforms.gff3.gz` for the 17 test species: the same genes with every isoform of the source release, plus the reference transcript where that release lacks its exact CDS. Each gene's isoforms equal the paper's any-isoform accepted set (`build_any_isoform.isoform_sets`) on 17/17 species.
- Medicago and Mimulus `genome.fa.gz` (+ `.fai`, `.gzi`) now hold the whole assembly (42 / 23 records, was 14 / 14 contigs >= 131 kb, which dropped 97 / 41 reference genes). The 14 records already hosted are byte-identical.
- Drops `plants/reference_curves.csv`, which nothing reads since the curves cell left notebook 03a.
Merge together with the ntv3_revised Space PR that switches the notebooks to the new reference name.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Add the 10 insect test species (benchmark references + soft-masked genomes) under insects/test_species/
