ehsanestaji · ehsanestaji · May 27, 2026 · May 26, 2026 · May 27, 2026 · May 27, 2026
diff --git a/AGENTS.md b/AGENTS.md
@@ -87,6 +87,44 @@ next: richer evidence tables for additional profiles and compare mode
 later: MCP/tool-agent interface and optional local summaries
 ```
 
+## Deep Release Vision
+
+Durable vision document:
+
+```text
+docs/vision-plan.md
+```
+
+FastaGuard should become the FASTA preflight operating system for modern
+bioinformatics pipelines: validate the FASTA, explain red flags, emit a stable
+contract, and route to the right downstream tools.
+
+The release strategy is evidence before expansion:
+
+```text
+v0.3: evidence pack + assembly gate + provenance checksums
+v0.4: compare mode for many FASTA files
+v0.5: transcriptome profile
+v0.6: protein profile
+v0.7: reference-panel profile
+later: MCP/tool-agent interface and optional local summaries
+```
+
+Default product boundaries:
+
+- stay fast and database-free by default
+- keep JSON as the source of truth
+- keep HTML as a human view
+- make findings machine-actionable with stable IDs, severity, evidence, thresholds, actions, and scope
+- keep optional generated summaries local-metrics-only and traceable back to structured fields
+- never claim to replace QUAST, BUSCO, BlobToolKit, CheckM, seqkit, MultiQC, or annotation workflows
+
+Recommended next big release:
+
+```text
+v0.3 should make FastaGuard credible as the default assembly gate before adding broad new biological profiles.
+```
+
 ## Collaboration Preference
 
 When moving the project forward, provide a clear recommendation first, then proceed when the user approves or explicitly asks to continue. The default recommendation should favor boring, stable contracts over flashy AI features.
diff --git a/README.md b/README.md
@@ -32,7 +32,8 @@ tar -xzf fastaguard-v0.2.0-x86_64-unknown-linux-gnu.tar.gz
 ```
 
 The v0.2.0 GitHub release binaries and source archive are published. Bioconda
-may still serve v0.1.1 until the upstream v0.2.0 recipe update is merged.
+serves v0.2.0 for Linux x86_64, Linux ARM64, macOS Intel, and macOS Apple
+Silicon.
 
 Local development build:
 
@@ -67,7 +68,7 @@ fastaguard --finding-catalog
 fastaguard --explain-finding high_n_rate
 ```
 
-Build and run the Docker image:
+Build and run the local Docker image:
 
 ```bash
 docker build -t fastaguard:local .
@@ -79,6 +80,12 @@ docker run --rm -v "$PWD:/data" fastaguard:local /data/sample.fa \
   --multiqc /data/fastaguard_mqc.json
 ```
 
+Use the generated BioContainers image in workflow engines:
+
+```bash
+docker pull quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+```
+
 Exit codes:
 
 ```text
@@ -160,12 +167,14 @@ FastaGuard catches FASTA-level assembly problems before expensive assembly QC.
 
 - [Example reports](examples/reports/README.md)
 - [Product thesis](docs/product-thesis.md)
+- [Vision plan](docs/vision-plan.md)
 - [MVP spec](docs/mvp-spec.md)
 - [Output contract](docs/output-contract.md)
 - [Tool landscape](docs/tool-landscape.md)
 - [Adoption plan](docs/adoption-plan.md)
 - [LLM and tooling vision](docs/llm-tooling-vision.md)
 - [Benchmarking](docs/benchmarking.md)
+- [v0.2 evidence pack](docs/evidence/fastaguard-v0.2-evidence.md)
 - [Packaging](docs/packaging.md)
 - [v0.2.0 release notes](docs/releases/v0.2.0.md)
 - [v0.1.1 release notes](docs/releases/v0.1.1.md)
@@ -175,7 +184,12 @@ FastaGuard catches FASTA-level assembly problems before expensive assembly QC.
 
 ## Status
 
-v0.2.0 is published on GitHub with Linux and macOS release binaries. The
-Bioconda v0.2.0 recipe metadata is ready with the published source archive SHA;
-Bioconda may still serve v0.1.1 until the upstream recipe update is merged.
-BioContainers image availability is still pending confirmation.
+v0.2.0 is published on GitHub with Linux and macOS release binaries. Bioconda
+serves v0.2.0 for `linux-64`, `linux-aarch64`, `osx-64`, and `osx-arm64`.
+BioContainers also publishes the pinned workflow image
+`quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0`.
+
+The next internal milestone is the
+[v0.2 evidence pack](docs/evidence/fastaguard-v0.2-evidence.md): reproducible
+local and public FASTA runs that document runtime, verdicts, and top findings
+before new biological profiles are added.
diff --git a/docs/adoption-plan.md b/docs/adoption-plan.md
@@ -8,21 +8,21 @@ adding many new biological heuristics.
 Priority:
 
 ```text
-Bioconda published -> BioContainers confirmation -> MultiQC plugin -> public benchmarks -> upstream workflow examples
+Bioconda published -> BioContainers available -> MultiQC plugin -> public benchmarks -> upstream workflow examples
 ```
 
 ## Phase 1: Package
 
 Goal: make installation natural for bioinformatics users.
 
-Status: Bioconda is live for FastaGuard v0.1.1, and the v0.2.0 recipe update
-is ready with the published GitHub source archive SHA.
+Status: Bioconda is live for FastaGuard v0.2.0 on Linux and macOS x86_64/ARM64
+platforms. BioContainers publishes the pinned workflow image
+`quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0`.
 
 - Keep GitHub release binaries working.
 - Keep Docker smoke tests passing.
 - Keep `packaging/bioconda/` aligned with the upstream Bioconda recipe.
-- Confirm BioContainers image/tag publication after the Bioconda merge;
-  current candidate tags are not yet visible in the registry.
+- Keep workflow examples pinned to the confirmed BioContainers image tag.
 
 Done when:
 
@@ -31,8 +31,8 @@ mamba install -c conda-forge -c bioconda fastaguard
 fastaguard --schema
 ```
 
-works in a clean environment. This has been verified locally on macOS for
-v0.1.1; repeat this check for v0.2.0 after the Bioconda update merges.
+works in a clean environment, and workflow engines can pull the pinned
+BioContainers image.
 
 ## Phase 2: Aggregate
 

diff --git a/docs/benchmarking.md b/docs/benchmarking.md
@@ -117,3 +117,30 @@ For each run, record:
 - whether downstream tools would have been blocked or recommended
 
 This evidence matters more than synthetic speed alone because it shows the wedge: cheap FASTA preflight before expensive downstream QC.
+
+## Evidence Pack Workflow
+
+The v0.2 evidence workflow is documented in
+`docs/evidence/fastaguard-v0.2-evidence.md`.
+
+CI-safe local run:
+
+```bash
+python3 scripts/collect_evidence.py \
+  --binary target/release/fastaguard \
+  --out-dir target/evidence/local-smoke \
+  --local-only
+```
+
+Public NCBI run:
+
+```bash
+python3 scripts/collect_evidence.py \
+  --binary target/release/fastaguard \
+  --out-dir target/evidence/v0.2
+```
+
+The public run uses NCBI Datasets commands such as
+`datasets download genome accession <ACCESSION> --include genome --filename <zip>`.
+It writes compact `evidence_summary.json` and `evidence_summary.tsv` files while
+leaving downloaded FASTA files and full reports under `target/`.
diff --git a/docs/evidence/fastaguard-v0.2-evidence.md b/docs/evidence/fastaguard-v0.2-evidence.md
@@ -0,0 +1,100 @@
+# FastaGuard v0.2 Evidence Pack
+
+This page records the evidence workflow for FastaGuard v0.2. It is intended to
+make the preflight claim inspectable before adding new biological profiles.
+
+FastaGuard is a FASTA preflight tool. It is not biological completeness
+analysis, not assembly correctness analysis, and not contamination confirmation.
+Passing FastaGuard means the FASTA-level contract is sane enough to route into
+downstream tools such as QUAST, BUSCO, BlobToolKit, CheckM, or annotation.
+
+## Local Evidence Run
+
+Build the release binary:
+
+```bash
+cargo build --release --locked
+```
+
+Run the CI-safe local evidence path:
+
+```bash
+python3 scripts/collect_evidence.py \
+  --binary target/release/fastaguard \
+  --out-dir target/evidence/local-smoke \
+  --local-only
+```
+
+Local-only mode does not require network access or the NCBI Datasets CLI. It
+runs:
+
+- a deterministic synthetic FASTA
+- `testdata/problem_assembly.fa`
+- a gzipped copy of `testdata/valid_assembly.fa`
+
+## Public NCBI Evidence Run
+
+Install the NCBI Datasets CLI, then run:
+
+```bash
+python3 scripts/collect_evidence.py \
+  --binary target/release/fastaguard \
+  --out-dir target/evidence/v0.2
+```
+
+The public workflow downloads genomic FASTA packages with commands shaped like:
+
+```bash
+datasets download genome accession GCF_000005845.2 --include genome --filename target/evidence/v0.2/ecoli_k12_mg1655/ncbi_dataset.zip
+```
+
+If `datasets` is not installed, the script exits before running public cases.
+Use `--local-only` for offline smoke tests.
+
+The default public manifest is:
+
+```text
+docs/evidence/public_assemblies.json
+```
+
+It currently includes:
+
+- `GCF_000005845.2`: Escherichia coli K-12 MG1655
+- `GCF_000182925.2`: Neurospora crassa OR74A
+
+## Outputs
+
+Each case writes FastaGuard artifacts under `target/evidence/<case>/`:
+
+- `fastaguard.json`
+- `fastaguard.tsv`
+- `fastaguard_report.html`
+- `fastaguard_mqc.json`
+
+The workflow also writes compact summaries:
+
+- `evidence_summary.json`
+- `evidence_summary.tsv`
+
+The summary records the command used, FastaGuard version, git commit, platform,
+date, input size, sequence count, elapsed seconds, verdict, and top findings.
+Commit the evidence page and compact summaries when useful. Do not commit
+downloaded FASTA files, NCBI zip archives, or full generated reports.
+
+## Interpretation
+
+Use this evidence to answer practical adoption questions:
+
+- how quickly does FastaGuard produce a preflight report?
+- does it catch duplicate IDs, invalid symbols, high-N records, and composition outliers?
+- does it produce JSON, TSV, HTML, and MultiQC-ready output before heavier tools run?
+
+Use QUAST, BUSCO, BlobToolKit, CheckM, sourmash, Kraken, or other tools for
+deeper biological interpretation after FastaGuard has checked the FASTA-level
+contract.
+
+## References
+
+- [NCBI Datasets genome download reference](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/datasets/download/genome/)
+- [NCBI Datasets genome download guide](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/download-genome/)
+- [Neurospora crassa OR74A BioProject](https://www.ncbi.nlm.nih.gov/bioproject/132)
diff --git a/docs/evidence/public_assemblies.json b/docs/evidence/public_assemblies.json
@@ -0,0 +1,19 @@
+{
+  "schema_version": 1,
+  "assemblies": [
+    {
+      "id": "ecoli_k12_mg1655",
+      "accession": "GCF_000005845.2",
+      "label": "Escherichia coli K-12 MG1655",
+      "category": "bacterial",
+      "source_url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/"
+    },
+    {
+      "id": "neurospora_crassa_or74a",
+      "accession": "GCF_000182925.2",
+      "label": "Neurospora crassa OR74A",
+      "category": "fungal",
+      "source_url": "https://www.ncbi.nlm.nih.gov/bioproject/132"
+    }
+  ]
+}
diff --git a/docs/packaging.md b/docs/packaging.md
@@ -9,10 +9,9 @@ Bioconda -> GitHub release binaries -> Docker image -> BioContainers -> Homebrew
 ```
 
 FastaGuard v0.2.0 is published on GitHub with Linux and macOS release binaries.
-Bioconda currently publishes v0.1.1 until the upstream v0.2.0 recipe update is
-merged. Docker remains useful for local smoke tests and pipeline containers,
-while BioContainers should be confirmed after the Bioconda publication pipeline
-catches up.
+Bioconda serves v0.2.0 on Linux and macOS x86_64/ARM64 platforms. Docker remains
+useful for local smoke tests, while BioContainers now provides the pinned
+workflow image generated from the Bioconda package.
 
 ## Bioconda
 
@@ -38,7 +37,7 @@ fastaguard --finding-catalog
 
 Current published package:
 
-- Version: `0.1.1`
+- Version: `0.2.0`
 - Platforms: `linux-64`, `linux-aarch64`, `osx-64`, `osx-arm64`
 - Package page: [anaconda.org/bioconda/fastaguard](https://anaconda.org/bioconda/fastaguard)
 
@@ -141,12 +140,14 @@ The Docker image should stay boring:
 
 That makes it easy to run in Nextflow, Snakemake, Galaxy, and CI systems.
 
-The Bioconda recipe has merged upstream. BioContainers should be confirmed
-separately by checking the generated registry image/tag once it appears. That
-path is preferable to maintaining a separate BioContainers Dockerfile unless
-automated container publication proves unavailable.
+The Bioconda recipe has merged upstream and generated a BioContainers image.
+Use the pinned tag in workflow examples:
 
-BioContainers image availability is still pending confirmation.
+```bash
+docker pull quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+```
+
+That path is preferable to maintaining a separate BioContainers Dockerfile.
 
 ## MultiQC
 

diff --git a/docs/releases/v0.2.0.md b/docs/releases/v0.2.0.md
@@ -17,14 +17,19 @@ pipelines.
 
 ## Install
 
-After the v0.2.0 Bioconda update merges, install it with:
+Install the v0.2.0 Bioconda package with:
 
 ```bash
 mamba install -c conda-forge -c bioconda fastaguard
 ```
 
 The v0.2.0 GitHub release binaries and source archive are published. Bioconda
-may still serve v0.1.1 until the upstream recipe update is merged.
+serves v0.2.0 for Linux and macOS x86_64/ARM64 platforms. BioContainers also
+publishes the pinned workflow image:
+
+```bash
+docker pull quay.io/biocontainers/fastaguard:0.2.0--hfa8f182_0
+```
 
 ## Positioning