Datasets:

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InstaDeepAI

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NTv3_annot_dataset

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InstaDeep Ltd 451

• 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.

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