Alignment And Mapping

Version Compatibility

Reference examples assume recent stable releases of the preferred tools, especially samtools 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 read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.

When To Use This Skill