dnadesign is a collection of modular bioinformatics tools for biological sequence design. It brings dataset management, sequence generation, assembly of designed or wild-type sequences into larger constructs, sequence-model inference, unsupervised analysis of learned sequence representations, optimization toward defined phenotypes, and cross-tool workflow orchestration into one repository.
Use the docs index to choose a workflow, inspect existing work, or jump to a tool.
- Docs index: main index for workflow, tool, and repository docs.
- Installation: bootstrap the environment and run baseline verification commands.
- Architecture, Design, Reliability, Security, Plans, Quality score: repository-level contracts and governance records.
- Developer docs: CI contracts, maintenance runbooks, and execution-planning references.
Use the tool READMEs below for task-specific docs and CLI entrypoints.
| Tool | Description | Coverage |
|---|---|---|
| usr | Inspect and manage USR datasets and Parquet-backed records. |  |
| ops | Plan, submit, and inspect batch runbooks across tools. |  |
| studies | Hold study-family adapters that read checked-in study records and plug family-owned observation/preflight logic into Ops. |  |
| notify | Send webhook notifications for local runs and scheduler-backed jobs. |  |
| densegen | Generate DNA sequence libraries from workspace configs and inputs. CLI: uv run dense. |
 |
| infer | Run sequence-model inference and write derived outputs back to datasets. |  |
| construct | Build template-based DNA constructs and record placement metadata. |  |
| opal | Run active-learning campaigns over labeled sequence datasets. |  |
| cluster | Cluster feature tables, render UMAPs, and write analysis outputs. |  |
| billboard | Measure regulatory diversity across DenseGen libraries. |  |
| libshuffle | Subsample libraries iteratively and analyze each round with billboard. |
 |
| nmf | Apply NMF to sequence libraries and summarize recurring TFBS combinations. |  |
| latentdna | Materialize workspace-owned latent views, samples, projections, and plots. |  |
| cruncher | Optimize sequences against PWM-driven objectives. |  |
| tfkdanalysis | Analyze TFKD libraries in PPTP-seq context. |  |
| aligner | Score global alignments with Biopython PairwiseAligner. |
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| baserender | Render sequences through a schema-driven adapter runtime. |  |
| contracts | Publish shared cross-tool artifact contracts without importing tool internals. |  |
| permuter | Generate sequence permutations and evaluate downstream outputs. |  |