All long-form documentation for DNAnalyzer lives here. Start with
ARCHITECTURE.md if you want the big picture and
REPOSITORY_MAP.md if you want to know where a specific
file lives.
| Doc | Purpose |
|---|---|
../AGENTS.md |
Orientation for agentic AI and automation |
ARCHITECTURE.md |
System diagrams and component responsibilities |
REPOSITORY_MAP.md |
Directory-by-directory guide |
API_REFERENCE.md |
REST and CLI reference |
| Doc | Purpose |
|---|---|
getting-started.md |
First-time setup |
Development_Environment.md |
Devcontainer and Codespaces |
migration-guide.md |
Migrating from the pre-REST-API CLI |
| Doc | Purpose |
|---|---|
usage/enhanced-features.md |
Preset modes, profiles, output organization |
usage/ancestry-snapshot.md |
Ancestry estimation from genotype exports |
usage/polygenic-risk-scoring.md |
PRS calculation walkthrough |
usage/package-session.md |
Archive a session's inputs and outputs |
samples/cli-arguments-examples.md |
Worked CLI examples |
| Doc | Purpose |
|---|---|
developer/GPU_Smith_Waterman.md |
Smith-Waterman implementation details |
developer/Plugin_Development.md |
Writing a DNAnalyzer plugin |
| Doc | Purpose |
|---|---|
research/genes.md |
Gene reference list |
research/genes-i2kmt.md |
Extended gene notes |
research/analysis-parameters.md |
Parameter choices and rationale |
| Doc | Purpose |
|---|---|
contributing/Contribution_Guidelines.md |
Contribution guide |
contributing/CONTRIBUTING.md |
Git workflow |
contributing/Code_Conventions.md |
Style rules |
| Doc | Purpose |
|---|---|
citations.md |
Academic citations |
history/ |
Archived design documents |
Simplified Chinese translations of the guides above are in i18n/.