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docs: expose runnable Binder and Colab paths #83

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11 changes: 10 additions & 1 deletion README.md
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Expand Up @@ -16,7 +16,9 @@ match, an ambiguous match, unmatched, or invalid.
[Getting started](https://dotmatch.readthedocs.io/en/latest/getting-started.html) ·
[Command reference](https://dotmatch.readthedocs.io/en/latest/command-reference.html) ·
[Examples](https://github.com/dnncha/dotmatch/tree/main/examples) ·
[Citation](https://dotmatch.readthedocs.io/en/latest/methods-and-citation.html)
[Citation](https://dotmatch.readthedocs.io/en/latest/methods-and-citation.html) ·
[Try the notebook in Binder](https://mybinder.org/v2/gh/dnncha/dotmatch/main?labpath=demo.ipynb) ·
[Try the notebook in Google Colab](https://colab.research.google.com/github/dnncha/dotmatch/blob/main/demo.ipynb)

![FASTQ reads and a target table are compared at a fixed read window. DotMatch writes counts, split FASTQs, QC tables, and reports.](https://raw.githubusercontent.com/dnncha/dotmatch/main/public/dotmatch-read-assignment.svg)

Expand All @@ -40,6 +42,13 @@ The Bioconda recipe supports Linux, Intel macOS, and Apple Silicon
(`osx-arm64`). If a newly tagged version has not reached Bioconda yet, use the
PyPI package or install from source.

The [Binder](https://mybinder.org/v2/gh/dnncha/dotmatch/main?labpath=demo.ipynb)
and [Colab](https://colab.research.google.com/github/dnncha/dotmatch/blob/main/demo.ipynb)
notebooks run a small synthetic smoke demo without requiring a local install.
Comment on lines +45 to +47

@chatgpt-codex-connector chatgpt-codex-connector Bot Aug 22, 2026

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P2 Badge Make the linked Colab notebook self-contained

When a user follows this Colab link, Colab loads the notebook but does not check out the surrounding repository. The setup cell in demo.ipynb searches the runtime working directory and its parents for demo-data/crispr_guides.tsv, so a standard /content runtime raises FileNotFoundError before the demo runs; the local dotmatch package would also be unavailable. Add a Colab bootstrap step that clones/installs the repository and selects its directory, or link to a notebook that includes such a step.

Useful? React with 👍 / 👎.

They check mechanics only, not biological validation. If you work with a
shareable or de-identified guide, barcode, or other fixed-target fixture, see
the [public validation request](https://github.com/dnncha/dotmatch/issues/82).

## A small example

Prepare a tab-separated target file:
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