Strain Tracking (bioSkills)

A Claude Code skill that resolves sub-species bacterial strains from shotgun metagenomes and tests whether two samples share the same strain — the analysis behind transmission, engraftment, and persistence claims.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT) — inStrain, StrainPhlAn, MIDAS2, StrainGE, metaSNV, dRep, Bowtie2 and skani are separately installed OSS
Capabilities Read/Write — Claude runs the skill’s workflow locally (Bash/Python), not as an MCP tool
Verified works · 2026-08-06
Security cleared · 2026-08-06 — GPTomics/bioSkills MIT, standard OSS deps, no advisories

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

  • Claude Code — clone and install via the bundled script: 
    git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "metagenomics"

    The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview the skills first.

  • Claude Code / other agents — copy just this one skill: 
    cp -r bioSkills/metagenomics/strain-tracking ~/.claude/skills/

    (run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). Install the chosen strain profiler and its reference genomes when prompted on first use.

What it does

Builds a reference set, profiles microdiversity, and compares strains across samples:

  • Workflow — dRep-dereplicate dataset MAGs to representative genomes (97–99% ANI) and build scaffold-to-bin metadata; Bowtie2-map sample reads to the concatenated reference; inStrain profile per sample to extract SNV populations and microdiversity; inStrain compare across samples using popANI (shared-strain threshold ≥99.999% over ≥50% genome breadth at ≥5× coverage); optionally MetaPhlAn + StrainPhlAn for marker-SNV consensus phylogeny and normalized genetic distance (nGD); skani for genome-to-genome ANI with the ~95% species boundary.
  • Method panel — inStrain (popANI/conANI population microdiversity), StrainPhlAn (marker-based cross-sample phylogeny), MIDAS2 (pan-genome SNVs plus gene copy-number variation), StrainGE (low-abundance strains down to ~0.5× coverage), metaSNV v2 (subspecies structure), and skani/fastANI/MASH for isolate and MAG comparison.

Primary use cases: transmission and engraftment inference (FMT, mother–infant, hospital outbreaks), strain persistence over time, isolate-to-metagenome matching.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally rather than as an MCP server. The upstream skill front-matter name is bio-metagenomics-strain-tracking; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /strain-tracking. Coverage is the binding constraint — the popANI shared-strain call requires ≥5× breadth-qualified coverage, so shallow surveys profiled with MetaPhlAn Profiling or Kraken Classification generally cannot be re-analysed at strain level without deeper sequencing. Upstream directory: metagenomics/strain-tracking.

Sources

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