long-read-genomicslisted

# Long-Read Genomics ## Version Compatibility Reference examples assume recent stable releases of the preferred tools, especially `long-read` and the other tools listed below. Before using code or command patterns, verify installed versions match the environment: - Python: `python -c "import <module>; print(<module>.__version__)"` - CLI: `<tool> --version` - If signatures differ, inspect the installed help or API and adapt the pattern instead of retrying unchanged. ## Overview Workflow for nanopore or PacBio long-read QC, alignment, polishing, methylation-aware analysis, and structural variant discovery. ## When To Use This Skill - use when the dataset is nanopore or PacBio long-read sequencing - use when structural variants, phasing, polishing, or long-read methylation are part of the task - use when long-read-specific QC and alignment assumptions must be respected ## Quick Route - If the input is raw or minimally processed data, start with validation and QC before any modeling. - If the input is already processed, skip directly to the first workflow step that matches the user goal. - If the user asks for a biological conclusion, always produce at least one QC or confidence artifact alongside the final result. ## Progressive Disclosure - Read `references/technical_reference.md` when you need deeper tool-selection rules, environment adaptation notes, or extra validation guidance. - Keep `SKILL.md` as the main execution path and load the reference file only when