MILESTONE
Milestone is a local, reproducible workflow for bacterial wgMLST analysis:
- schema creation or public schema import
- allele calling
- profile comparison (
pairwise,batch,matrix) - schema QC and benchmark workflows
- publication-ready packaging and reporting
- Streamlit web UI for interactive runs
Live static site: https://fatmakahveci.github.io/milestone/
Quick Start
CLI setup
python -m venv .venv
source .venv/bin/activate
pip install -r webapp/requirements.txtRun web app
streamlit run webapp/app.pyRun tests
pytest testsCore Commands
1) Compare two profiles
python workflow/milestone.py profile_compare \
--profile-a output/run_a/sample_a_wgmlst.tsv \
--profile-b output/run_b/sample_b_wgmlst.tsv \
--output-dir output/compare/sample_a_vs_bOutputs:
wgmlst_profile_summary.jsonwgmlst_profile_comparison.tsv
2) Build profile distance matrix
python workflow/milestone.py profile_matrix \
--profiles output/run_a/sample_a_wgmlst.tsv output/run_b/sample_b_wgmlst.tsv output/run_c/sample_c_wgmlst.tsv \
--output output/compare/matrix_abcOutputs:
wgmlst_distance_matrix.tsvwgmlst_distance_summary.jsonwgmlst_distance_report.html
3) Benchmark against truth profiles
python workflow/milestone.py profile_benchmark \
--predicted-dir output/predicted_profiles \
--truth-dir validation/truth_profiles \
--output output/benchmark_runOutputs:
wgmlst_benchmark_summary.jsonwgmlst_benchmark_per_sample.tsvwgmlst_benchmark_per_locus.tsvwgmlst_benchmark_report.html
4) Schema QC
python workflow/scripts/schema_qc.py \
--schema-dir tests/fixtures/smoke_schema \
--output-dir output/schema_qcOutputs:
schema_qc_summary.jsonschema_qc_issues.tsv
Public Schema / Benchmark Import
PubMLST scheme import
python workflow/scripts/import_pubmlst_scheme.py \
--database pubmlst_neisseria_seqdef \
--scheme-id 1 \
--output-dir schemas/neisseria_wgmlst \
--include-profilesPubMLST benchmark pack import
python workflow/scripts/import_pubmlst_benchmark_pack.py \
--scheme-database pubmlst_neisseria_seqdef \
--isolate-database pubmlst_neisseria_isolates \
--scheme-id 1 \
--isolate-id 101 \
--isolate-id 102 \
--species "Neisseria meningitidis" \
--output-dir benchmark_packs/neisseria_demoEnteroBase scheme import
python workflow/scripts/import_enterobase_scheme.py \
--database senterica \
--scheme-name wgMLST \
--output-dir public_schemes/enterobase_sentericaIf EnteroBase requires authentication, set one of:
export ENTEROBASE_TOKEN="..."or
export ENTEROBASE_USERNAME="..."
export ENTEROBASE_PASSWORD="..."Publication / Validation Utilities
python workflow/milestone.py publication_readiness \
--schema-qc-summary results/schema_qc/schema_qc_summary.json \
--benchmark-summary results/benchmark/wgmlst_benchmark_summary.json \
--schema-manifest results/schema/schema_manifest.json \
--output results/publication_readinesspython workflow/milestone.py publication_package \
--schema-qc-summary results/schema_qc/schema_qc_summary.json \
--benchmark-summary results/benchmark/wgmlst_benchmark_summary.json \
--schema-manifest results/schema/schema_manifest.json \
--output results/milestone_publication_package.zip \
--title "Milestone validation package"Docker
Full stack
docker compose up --buildUI only
docker compose up --build milestone-webRuntime image with full bioinformatics stack
docker compose up --build milestone-runtimeExternal tool smoke benchmarking
docker compose run --rm milestone-benchmarkProject Documentation
- What Milestone Is
- How To Use Milestone
- Publish Web Demo
- Competitive Analysis
- Public Benchmark Datasets
- Publication Checklist
- Publication Runbook
- Manuscript Sections
- External Tool Benchmarking
- External Tool Install Notes
Notes
- Milestone outputs
*_wgmlst.tsvprofile files. - Profile comparison is a schema-based discriminator; it is not a direct phylogeny engine.
- Species-specific validation is still required before strong biological claims.