Contig
Contig

MVP · early access

Contig

An agentic bioinformatics analyst: it runs the analysis, fixes what breaks, and proves the result.

Contig takes raw sequencing data all the way to a verified, reproducible answer: it selects and runs the right pipeline on your own compute, diagnoses and self-heals failures, verifies the output, and writes a portable record anyone can reproduce.

View on GitHub Latest release

quickstart

# Python, any OS with Python 3.12+
pipx install contig

# run → self-heal → verify → reproduce
contig run --run-id smoke

# verdict + provenance + repair chain
contig show smoke

No data of your own needed — the smoke run uses nf-core/rnaseq's bundled test profile. From a source checkout, prefix each command with uv run.

01 Why

The hard part isn't turning English into a workflow.

Producing an end-to-end analysis from raw sequencing data needs a rare pairing of domain biology and computational engineering.

74%

Roughly 74% of wet-lab scientists have no programming experience

arXiv 2507.20122

Turning English into a workflow is the easy, crowded part. Running it, fixing it, and proving it is the unsolved part, and that's Contig.

02 What it does

Four things no incumbent does, on your own compute.

  1. Goal → pipeline, vetted

    Describe your goal in plain language; Contig proposes a curated pipeline and params to approve, and flags problems (no replicates, single-end, missing reference) before a multi-hour run.

  2. Self-healing runs, with an approval gate

    When a step fails (OOM, a missing index it can build, version mismatch, malformed input), Contig diagnoses it, applies a safe patch and retries, showing you the repair chain. A risky fix pauses the run for your approval instead of guessing.

  3. Verified outputs, per assay

    Every run ends in an honest verdict — PASS, WARN, FAIL or UNVERIFIED — backed by real checks, never a bare “done”. contig show --explain names the exact checks that drove it.

  4. Reproducible by default

    Each run pins inputs (checksums), pipeline revision, params and tool versions into a portable record. Your reads never leave your machine; only hashes are recorded.

03 A closer look

Real commands, real terminal output.

Contig self-heals a stale aligner index: STAR_ALIGN fails, Contig diagnoses missing_index, rebuilds the index and retries, returning PASS.
Self-heal a broken step — diagnose, patch, retry, unattended.
Contig verify's layered verdict: QC thresholds, structural checks, cross-tool concordance, biological plausibility and output-integrity re-hashing all passing.
A verdict you can trust — independent checks, honestly scoped per assay.
A real terminal capture: a run hits an out-of-memory failure, self-heals, passes QC to a PASS verdict, and produces a signed, reproducible record.
One run: OOM → self-heal → PASS verdict → signed, verified record.

04 The verdict

Never a bare “done”.

Every run ends in one of four verdicts, drawn from QC-metric thresholds, structural and integrity checks on the output files, cross-tool concordance, and biological-plausibility checks.

  • PASS

    Ran to completion and every QC check passed.

  • WARN

    Completed, but a QC check is borderline; look before you trust it.

  • FAIL

    A task or QC check failed; do not trust the output.

  • UNVERIFIED

    Completed, but nothing checked it, so we won't claim it's correct.

The scoping rule

Verification is scoped honestly per assay and never over-claims: a check earns a FAIL band only where a grossly-wrong value is distinguishable from unusual-but-real science — so an empty call set FAILs, while a low-purity tumour's VAF stays a WARN, and UNVERIFIED never masquerades as either.

05 Status & limits

MVP engine built; in early access.

What works today

The Layer-2 core — run → capture → self-heal → verify → reproduce — works end-to-end on nf-core/rnaseq, as a CLI and a local dashboard. The other assays ship a curated pipeline plus an assay-aware QC pack and are being hardened toward the same bar.

Verification scope varies by assay

nf-core/rnaseq is exercised end-to-end, including the self-heal loop, in CI. For other assays the checks are scoped to what that assay makes distinguishable — no verdict claims more than its checks support.

Laptop or cloud

One command lands unchanged on Docker locally or AWS Batch in your own account, via Nextflow's native executors. The dashboard is localhost-only today.

License

Apache License 2.0 — permissive, with an explicit patent and trademark grant. Use, modify and redistribute Contig, including commercially, under its terms. Third-party pipelines keep their own licenses.