CD-HIT in Google Colab

The CD-HIT web server has been unavailable since 2022, which left many users without an easy way to cluster sequences and remove redundancy. As an alternative, I wrote a Google Colab notebook that builds CD-HIT from source and runs it on your own sequences, entirely in the browser.

All parameters are form fields with explanatory notes, so a saved copy of the notebook records exactly what was run. Each run also writes a provenance file with the CD-HIT version, the full command line, an input checksum and a timestamp. The notes also explain two options that are often confused, -s (minimum length ratio) and -aS (alignment coverage of the shorter sequence).

Open in Colab · GitHub · Zenodo: 10.5281/zenodo.23503573