tracking-taxonomy-updateslisted

# Tracking Taxonomy Updates Use authoritative sources to report taxonomy changes with explicit versions, dates, and provenance. ## Instructions 1. Determine scope (domain, timeframe, output type). 2. Pull authoritative updates and release notes. 3. Extract versioned changes and impacts. 4. If assigning taxonomy for any assembly, MAG, SAG, isolate genome, bin set, or contig FASTA, start with a QuickClade first-pass domain screen through the BBTools container. Save both per-input and `percontig` results before choosing downstream tools. 5. Route from the QuickClade domain screen: - Bacteria or Archaea -> run GTDB-Tk for genome taxonomy. If the GTDB-Tk reference package is missing, set up/download it under the project/reference DB root, set `GTDBTK_DATA_PATH`, and record the release before running classification. - Viral or virus-like -> route to `/bio-viromics`; use vConTACT3 for phage/prokaryotic-virus gene-sharing taxonomy and GVClass for giant-virus/Nucleocytoviricota candidates. - Eukaryota -> run EukCC for eukaryotic MAG/genome QC and taxonomy context. - Mixed, low-confidence, or conflicting domains -> split or flag contigs for manual review before domain-specific classification. 6. Normalize IDs and taxonomy strings across tools. Convert QuickClade machine output with `scripts/quickclade_to_routing.py` so every downstream decision uses the documented `domain_routing.tsv` schema. 7. Deliver a versioned report with conflicts flagged. 8. Submit GTDB-T