AI integration

This page describes ways to use SemiBin together with AI assistants: an interactive chat bot that can answer questions about SemiBin, and an agent skill that teaches coding agents how to drive SemiBin2 correctly.

Ask the SemiBin chat bot

If you have a question about SemiBin — how to run it, what a particular option does, how to interpret the output, or how to troubleshoot an error — you can ask our NotebookLM-powered chat bot, which has been given the SemiBin documentation as its source material:

➜ Chat with the SemiBin assistant

The bot answers from the SemiBin documentation and cites the sections it draws from, so you can follow up in the docs themselves. It is a good first stop for "how do I…?" questions.

The SemiBin agent skill (for coding agents)

SemiBin ships with an agent skill that teaches coding agents (such as Claude Code) how to use SemiBin2 correctly: which subcommand to pick for each binning mode, how to validate inputs, where the output bins are written, and how to resolve common errors. When the skill is installed, an agent working in your project can pick the right command and flags on the first try instead of guessing.

Installing the skill

Use the install-skills subcommand. By default it installs into the current project (./.claude/skills), so an agent working in that directory finds it automatically:

SemiBin2 install-skills

To install it once for your user account (available in every project), install into $HOME/.claude/skills instead:

SemiBin2 install-skills --user

You can also point it at an explicit directory with --skills-dir. See the install-skills subcommand reference for details.

What the skill covers

• Choosing between single-sample, co-assembly, and multi-sample binning.
• Building correct command lines (including long-read and pre-trained-model workflows).
• Validating inputs (sorted/indexed BAM files, uniquely named contigs, the multi-sample separator).
• Where the final bins and summary tables are written.
• Fixes for the most common error messages.

The skill is bundled inside the installed SemiBin package, so the copy you install always matches the version of SemiBin you are running.

We want your feedback

These AI integrations are new and we are very interested in hearing how you use them. In particular, if the chat bot or an AI agent using the skill ever gives you bad, misleading, or outdated advice, please let us know: that kind of report is extremely valuable and helps us improve the documentation and the skill.

Please share your experience (good or bad) through the GitHub issue tracker or the SemiBin users mailing list.