Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
Notebooks: consolidate atlas+ClinVar, redesigned analyses; perf threads {1,2,4,8,16}; drop removed-notebook links
Perf: one headline (~970x end-to-end), drop warm-map multipliers; short Docker section
Repo reorg: parsing/, software_tests/, tutorial/{examples,reproduce_paper/{benchmarks,end_to_end}} — update all paths
fetch Zenodo-only wording; plain Windows note; drop Docker/smoke; consolidate benchmark tables (1M threads×batch grid); custom-GTF stdout-only
Performance page: VisProDom/geneplot numbers now on the human v86 set Both run on the same human Ensembl-86 set instead of their bundled maize/fruit-fly examples: VisProDom 42.7 s / 2.3 GB (rebuilds the genome per call), geneplot ~14 genes/s (gffutils DB + per-gene domain re-read).
Performance page: fresh GenomicFeatures/VisProDom numbers, correct geneplot (it does map)
Rename benchmarking.ipynb link to scaling_and_ram.ipynb (self-benchmark)
Point Performance page at validation/software_comparison notebooks; add walkthrough nbviewer link The combined proteintogenome_comparison.ipynb is being split into validation.ipynb (accuracy) + software_comparison.ipynb (speed); repoint the accuracy and speed sections accordingly. Add a walkthrough nbviewer link on the Tutorials page since its interactive viewers don't render on GitHub.
Fix index docs: Home fetch path, drop bogus human-v115 row, 298 MB index, Plotting segments import - Home quickstart: 'fetch human --out human.idx' so the next map step's --index human.idx actually resolves (fetch defaults to ~/.cache). - Drop the fabricated 'human-v115 / ensembl_v15_human.idx' pre-built row (no such Zenodo target). - Performance: human GENCODE index is ~298 MB, not 128 MB. - Plotting: import _segments_from_dataframe from prot2exon.plot instead of the broken p2e.plot.<attr> path.
Performance: point validation/comparison links to the live proteintogenome_comparison notebook
Performance: add GenomicFeatures + VisProDom comparators (3-way 100% agreement; speed/RAM)
Restructure wiki into a sequential 7-section workflow Install -> Building an index -> Mapping -> Plotting -> Tutorials and notebooks -> Performance and benchmarking -> Reference. Merge the old scattered pages (Genome-onboarding + Custom-proteins -> Index; Output-modes + Input-format -> Mapping; Performance-and-RAM + Validation + Benchmarks -> Performance and benchmarking); drop the standalone Quickstart and CLI-reference. Update all CLI to the four-command form (index / map / fetch / plot) and the fetch-defaults-to-Zenodo model. Sidebar lists each section's subsections.