osmo_refdb: a DIAMOND+HMM reference database for osmoadaptation gene detection in metagenomic data

Reference DIAMOND (protein sequence search) and HMM (profile hidden Markov model) database for detecting osmoadaptation genes in metagenomic sequencing data, for use with osmotool. Covers 43 gene families spanning compatible-solute transport and biosynthesis (glycine betaine, proline, carnitine, choline, trehalose), Na⁺/K⁺ transport and antiporter complexes, mechanosensitive channels, glutathione redox cycling, cold-shock response, and related stress-response genes — including a dedicated Firmicutes/Bacillota gap-filling panel (Bacillus-type Opu transporters, the Mrp/Mnh Na⁺/H⁺ antiporter complex substituting for nhaA, and the Ktr K⁺-uptake system substituting for Trk) added to close phylum-level detection gaps in the original panel: - Ectoine synthesis: ectA, ectB, ectC- Trehalose synthesis: otsA, otsB- Glutathione redox cycle: gshA, gshB, gshF, gor- Choline → glycine betaine oxidation: betA, betB- Compatible-solute transporters: betL, proX, proP, opuAA, opuBA, opuCA, opuAB, opuBB, opuCB, opuAC, opuBC, opuCC- Mrp/Mnh Na⁺/H⁺ antiporter complex: mrpA, mrpB, mrpC, mrpD, mrpE, mrpF, mrpG- Other Na⁺/H⁺ and K⁺ transport: nhaA, kdpA, trkA, trkH, ktrA, ktrB, ktrD- Mechanosensitive channels: mscL, mscS- Housekeeping / co-occurrence markers: galE, mazG, murB- Cold shock: cspA Reference sequences curated from UniProt, with per-family gene-symbol queries checked for common annotation gaps (documented synonyms, organism-specific numbered paralogs). Six families with a Pfam domain confirmed gene-specific via InterPro (mrpB, mrpE, mrpF, mrpG, gshB, cspA) use that Pfam family's own curated HMM and gathering (GA) cutoff directly rather than a locally built model. Six families (murB, otsA, mrpC, trkH, ktrB, ktrD) are built and searchable for genome-level co-occurrence checks (`osmotool annotate`) but excluded from `osmotool profile`'s reported read-level output, after benchmarking showed their negative reference pools are structurally contaminated by real, unlabeled orthologs in a way no amount of additional curation resolves — a limitation documented per-family in this release's `qc_scorecard.tsv` and in the source repository's README, not hidden. Per-family score cutoffs calibrated against held-out sequence data and validated against both simulated and real-genome short reads. Contents:- osmo_refdb.dmnd — DIAMOND protein database- hmms/osmo_refdb.hmm (+ .h3f/.h3i/.h3m/.h3p) — pressed HMM database with per-family gathering (GA) cutoffs- osmo_refdb.diamond_cutoffs.tsv, osmo_refdb.profile_cascade.tsv — per-family DIAMOND cutoffs and the DIAMOND+HMM cascade configuration used by osmotool profile- osmo_refdb.profile_excluded_families.txt, osmo_refdb.annotate_excluded_families.txt — families excluded from reported output in each osmotool mode- refs/, alignments/, results/, qc_scorecard.tsv — full build and benchmark provenance (QC'd reference sequences, alignments, per-family precision/recall/F1 benchmark output), included for reproducibility Built with osmo_refdb (pipeline source + full documentation, including a full build changelog and per-family design rationale). Licensed under MIT.